Tomales Bay Watershed Stewardship Plan: A Framework for Action

Prepared by: Tomales Bay Watershed Council

July 2003

When citing or referring to this plan please use the following: The Tomales Bay Watershed Stewardship Plan: A Framework for Action. Tomales Bay Watershed Council, July 2003. 137 pp.

Cover photo courtesy of Marty Knapp, www.martyknapp.com

Funding for this Plan was provided by the California State Coastal Conservancy; Marin Community Foundation; David L. Klein, Jr. Foundation; County of Marin; California Department of Fish and Game, Salmon and Steelhead Trout Restoration Account; and local private donors.

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Tomales Bay Watershed Stewardship Plan Endorsement We, the undersigned members of the Tomales Bay Watershed Council, have worked together to develop the strategies and recommendations contained in the Tomales Bay Watershed Stewardship Plan. When the document becomes final, after public review, we intend to continue working together to restore, enhance and protect the Tomales Bay watershed. The strategies in this document are intended to be used by agencies and community members either individually or collectively to improve management of Tomales Bay.

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Table of Contents Acknowledgements…………………………………………………. List of Contributors, Editors and Technical Reviewers…………….. Executive Summary………………………………………………… List of acronyms and abbreviations used in this Plan………………. I.

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INTRODUCTION………………………………………………………….…

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1.0 Tomales Bay Watershed Council Formation and Vision…………………. 2.0 Past Accomplishments in the Tomales Bay Watershed…………..…….…. 3.0 Federal, State and Local Watershed Conservation Legislation …… 3.1 Federal laws……………………………………………………… 3.2 State laws………………………………………………………… 3.3 County laws………………………………………………………. 4.0 Watershed Conservation and Stewardship ……………………………….

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WATERSHED CHARACTERIZATION…………………………………..

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A. DESCRIPTION OF THE TOMALES BAY WATERSHED…………….. . 1.0 General description …………………………………………………… 1.1 Summary of watershed reports and studies…………………... 2.0 Special Recognition of Tomales Bay ………………………………… 3.0 Physical Description …………………………………………………. 3.1 Tomales Bay………………….. ……………………………. 3.1.1 Freshwater inflow………………………….…… 3.1.2 Circulation, sedimentation, nutrient levels and water borne pathogens…..……………………………. 3.2 Catchment area and tributaries……………………………… 3.3 Climate……………………………………………………… 3.4 Geology..……………………………………………………. 3.5 Soils ………………………………………………………… 3.6 Fire History ………………………………………………… 3.7 Biological Resources………………………………………... Literature cited……………………………………………………………

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B. HUMAN USES OF NATURAL RESOURCES………………………… 1.0 Introduction …………………………………………………………. 2.0 Residential Development, Water Supply and Waste Management ... 3.0 A Historical Overview of Land Use in the Watershed ……………… 3.1 History of agriculture in the watershed ………………….… 3.2 History of mercury mining in the Walker Creek watershed… 3.3 History of logging, reservoirs and development in the Lagunitas Creek watershed ……………………………………………. 4.0 Mariculture ………………………………………………………….. 5.0 Recreational Uses …………………………………………………… 6.0 Open Space ………………………………………………………….. 6.1 Non-agricultural open space ………………………………...

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6.2 Parks in the watershed ……………………………………… 6.2.1 Federal parks …………………………………… 6.2.2 State parks ……………………………………… 6.2.3 County parks …………………………………… 6.2.4 Other parks……………………………………… 6.3 Reserves ……………………………………………………... 7.0 Fisheries …………………………………………………………….. 7.1 Commercial fisheries ………………………………………. 7.2 Recreational fisheries ………………………………………. Literature cited…………………………………………………………… III.

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A FRAMEWORK FOR WATERSHED STEWARDSHIP………………

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A. GOALS AND OBJECTIVES ………………………..…………………..

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B. ACTION PLAN ………………………………………………………….

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ACTION 1.0 Develop a coordinated and comprehensive water quality monitoring plan for Tomales Bay and tributary streams…….…..……….

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ACTION 2.0 Support implementation of practices and projects that will reduce nonpoint sources of water pollution and enhance habitats in Tomales Bay and its watershed……….…………………………………

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ACTION 3.0 Assess, protect and restore key habitats for species of local interest……………………………………………………………...……..

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ACTION 4.0 Promote and support public outreach and education about Tomales Bay and its watershed………………………………………….

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ACTION PLAN IMPLEMENTATION……………………………………

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A. Partnerships and Collaboration………………………………………….. B. Future Steps for the Tomales Bay Watershed Council…………………… 1.0 Council priorities …………………………………….……. 2.0 Administrative activities …………………………………...

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APPENDICES ………………………………………………………………

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A. Water Quality Status and Trends Report…………………………………

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B. Erosion and Sedimentation in the Tomales Bay Watershed……………..

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C. A Glossary of Common Ecological and Watershed Related Terms…….

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D. Summary Responses to Public Comments………………………………

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Maps, Figures and Tables Figure 1. Map of the Tomales Bay watershed……………………………………. Table 1. Tomales Bay Watershed Council Priorities 2003-2005…………………

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Acknowledgements We would like to thank the following individuals for their participation and contribution during on-going committee meetings, or in the completion of specific and necessary tasks during the last three years, as we developed this plan together. We would also like to thank so many others who gave unselfishly of their time. Jerry Abbott, Inverness Yacht Club Sarah Allen, Point Reyes National Seashore Tom Baty, Local Resident Bob Berner, Marin Agricultural Land Trust Marc Commandatore, California Department of Health Services John Dell’Osso, Point Reyes National Seashore Nicholas Dewar, Process support and facilitation Jules Evens, Avocet Research Associates George Jenkins, Local Resident Lynnette Kahn, West Marin Chamber of Commerce Brannon Ketcham, Point Reyes National Seashore Steve Kinsey, Marin County Supervisor Michael Lennox, U.C. Cooperative Extension David Lewis, U.C. Cooperative Extension Dave Matthews, California State Parks Julie Monson, League of Women Voters Scott McMorrow, Webmaster Sita Mulligan, Marin Resource Conservation District Richard Plant, Tomales Bay Advisory Committee Carlos Porrata, California State Parks David Press, Point Reyes National Seashore Liza Prunuske, Prunuske Chatham, Inc. Annelore Reisewitz, Consultant Nancy Scolari, Marin Resource Conservation District Sheila Semans, State Coastal Conservancy Harry Seraydarian, U.S. Environmental Protection Agency Ellen Straus, Dairy Rancher Rebecca Tuden, Marin County/RWQCB/U.S. EPA Nelia White, S.F Regional Water Quality Control Board Dyan Whyte, S.F Regional Water Quality Control Board Tom Yarish, Local Resident

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Technical Reviewers: Sarah Allen Senior Science Advisor National Park Service Point Reyes National Seashore, California

Contributors: Neysa King, Coordinator Tomales Bay Watershed Council Point Reyes Station, California Liza Prunuske Prunuske Chatham, Inc. Occidental, California

Jules Evens Avocet Research Associates Point Reyes Station, California

Ed Smith Prunuske Chatham, Inc. Occidental, California

John Kelly Audubon Canyon Ranch, Cypress Grove Research Center Marshall, California

Tom Baty Inverness, California

David Lewis, Watershed Management Advisor University of California Cooperative Extension Santa Rosa, California

Alexis Suarez Point Reyes Station, California

Dyan Whyte San Francisco Bay Region, Regional Water Quality Control Board Oakland, California

Editors: Catherine Caufield Environmental Action Committee of West Marin Point Reyes Station, California David Lewis, Watershed Management Advisor University of California Cooperative Extension Santa Rosa, California

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EXECUTIVE SUMMARY “When you come over some low summit or around some curve of road and find that you are looking at Tomales Bay – whether for the first time or for the five-thousandth time — you know that you have come to a place that is valuable and strange. This flooded rift, blue under sunlight or gray under fog, always takes you partly by surprise.” -- John Hart, A Sense of Place, Tomales Bay Environmental Study, 1972

The Tomales Bay watershed is remarkable for its beauty, wildlife, and diverse human history. At the juncture between the ocean and the land, Tomales Bay is created by the San Andreas Fault and underlying geology. The result is a striking contrast between the oak woodland and open grasslands to the east of the Fault, with dark and thick conifer and hardwood forests to the west. Many people who live here and those who come to visit are deeply connected to and inspired by the rolling hills, forests, beaches and cool waters, marshes and meadows of this watershed. For both human and non-human communities that live here, and for others that migrate through, Tomales Bay and the surrounding watershed is a refuge. Tomales Bay watershed includes a broad diversity of both aquatic and terrestrial habitats. An abundance of plant and animal life depends on habitats in the bay and surrounding watershed for shelter, foraging, nesting and rearing needs. Nearly 900 species of plants, 490 species of birds, hundreds of invertebrate species, and numerous sensitive, threatened and endangered species inhabit the watershed and nearby Point Reyes peninsula. Sensitive species include federally listed species such as coho salmon, steelhead trout, brown pelican, Steller sea lion and red-legged frog. Other sensitive species that have state or local significance include tule elk, Point Reyes jumping mouse, and river otter, as well as numerous endemic and rare plants. During the last two centuries, the watershed’s rich natural resource base has supported a local agricultural community, mariculture industry, and commercial and recreational fisheries that have provided high quality products both locally and to the San Francisco Bay Area and beyond. Today, the region has a resident population of approximately 11,000 people, mostly clustered in eleven villages. Residents continue to share in a continuation of food production and local self-reliance through local creameries, cheese makers, organic farms and other agricultural production systems; the local oyster industry; and the collection of firewood, berries, herbs and other goods. Additionally, much of the local economy has shifted and is predicated upon the demand for recreation-oriented goods and services ranging from overnight accommodations to kayak rentals to numerous eateries that serve approximately 2.5 million visitors annually. Visitors make trips to the Point Reyes National Seashore, take boating excursions on the bay, go birdwatching, hike hills and valleys, and frequent local restaurants and markets. Past and present human uses of the Bay and watershed have had significant cumulative impacts on water quality, habitats, and species, resulting in a need for comprehensive Tomales Bay Watershed Stewardship Plan: A Framework for Action 1

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watershed management. Sedimentation from tributary streams has reduced the area of the bay over the last 200 years. Salmon habitat has been diminished to less than half of the original range, and remaining habitat has been compromised by human activities over the last century. During recent years, water quality monitoring has resulted in the posting of human health advisories for the bay and tributaries for water contact, and the consumption of seven species of sport fishes regularly caught in Tomales Bay. Human activities that have affected the watershed include: residential development, agriculture, forestry, impoundment of water and the creation of large-scale reservoirs, mining, recreation, road construction, septic and waste disposal, and shellfish harvesting. Comprehensive watershed management or watershed stewardship must consider all of the ecosystems that comprise a watershed, and many dynamic interactions between these natural systems. Effective management understands, respects, and works with natural processes. Due to the complexity of these systems, watershed planning requires an inter-disciplinary, stakeholder-based process for natural resource management. In California and elsewhere, councils have been created to develop watershed-based strategies to protect and restore habitats and open space, while promoting sustainable land-use practices and the health of coastal watersheds. The Tomales Bay watershed is a place of riches - a place that is both beautiful and livable for its residents and visitors. In order to protect and restore the health and vitality of the bay and watershed community, local residents have joined public agencies and conservation organizations to form the Tomales Bay Watershed Council. Together, we have developed this Watershed Stewardship Plan. By working together with an expanded sense of community, we can protect the aquatic and terrestrial habitats that are essential to Tomales Bay as well as preserve the culture and heritage of the region. Past accomplishments that preceded the creation of the Council and this Plan include: the preservation and protection of open space and agricultural lands, implementation of soil and water conservation projects, and the restoration of aquatic and riparian habitats. These efforts have contributed to the relatively healthy natural state of our bay and watershed, and to the viability of local enterprises and small communities. These efforts also demonstrate the considerable local, regional, and national capacities and commitments to protect and preserve many of these shared watershed values. The future of many of these values will depend on our diligence in continuing and hopefully expanding these conservation, preservation and restoration efforts. This plan is intended to communicate and guide actions to achieve our shared vision for the bay and watershed. The Tomales Bay Watershed Council has 24 members that are drawn from local stakeholder groups and agencies affected by or responsible for the watershed, including: 1) residential and community groups, 2) agricultural interests, 3) environmental groups, 4) maricultural interests, 5) recreational interests and 6) public agencies. The aim is to provide a continuing, collaborative forum that will improve local capacity to comprehensively manage and protect the watershed, Tomales Bay, and the interests of these stakeholders. More specifically, Council members are committed to a watershed wherein:

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• • • • • •

human activities in the watershed -including agriculture, recreation, commercial fishing, and residential use - coexist with high, sustainable or improving levels of ecosystem health and watershed function; natural habitats and a broad diversity of wildlife species, including salmonid populations, are restored throughout the watershed; water quality of the Bay and its tributaries meets State standards for shellfish mariculture (as a benchmark for clean water); sustainable agriculture is one of the primary land uses in the watershed; the rural character and quality of life for local residents and communities is preserved; and the public participates in planning and managing the watershed.

To achieve this shared vision, the Council has written this Plan to address human activities that affect water quality and habitats in Tomales Bay and its watershed. This Plan also makes recommendations to improve natural resource management that recognizes and supports beneficial watershed activities. More specifically the goals of the Plan are to: • • •

Ensure water quality in Tomales Bay and tributary streams sufficient to support natural resources and beneficial uses; Restore and preserve the integrity of natural habitats and native communities; and Develop strategies to implement the Plan and to protect the watershed.

To achieve these goals, we recommend the following four actions: Action 1.0

Develop a coordinated and comprehensive water quality monitoring plan for Tomales Bay and tributary streams: Clean water is essential to both aquatic and terrestrial environments. In the Tomales Bay watershed, water quality and healthy aquatic habitats are influenced by tidal circulation, by activities that occur nearby on land, and by pollutants delivered via surface run-off and subsurface seepage. A comprehensive long-term monitoring program is needed to document baseline conditions and identify trends for pollutants of concern. This program would provide the information needed to evaluate water quality in the Bay and its tributaries, as well as the efficacy of educational programs, projects to reduce non-point sources of pollution, and management practices intended to improve water quality. With a database to determine action efficiency in place, management and conservation strategies and future actions in the watershed will be based on the most current and best available monitoring data.

Action 2.0

Support implementation of practices and projects that will reduce nonpoint sources of water pollution and enhance habitats in Tomales Bay and its watershed: During the past 20 years, significant steps have been taken on private and public lands to improve water quality and aquatic and terrestrial habitats in the Tomales Bay watershed. The momentum that has been created by partnerships between private landowners, local organizations

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and agencies has resulted in an increased understanding of water quality issues, the condition of Tomales Bay and tributary streams, and linkages between sources of pollutants and water quality. In addition, these activities have improved local awareness about native habitats in the Bay and watershed. Despite decades of individual efforts, significant problems remain. To address these issues, future collaboration will be necessary to maintain this progress and to increase these local programs. Action 3.0

Assess, protect and restore key habitats for species of local interest: According to a recent report by the California Department of Fish and Game, habitat destruction and exotic species are the two largest threats to the survival of endangered species. Although some habitats in the Tomales Bay watershed are relatively healthy, many have been seriously compromised and need to be restored and protected. For example, the construction of large dams and reservoirs in the Lagunitas and Walker Creek watersheds has resulted in the loss of more than half of the historic spawning grounds for coho salmon and steelhead trout. Development, sedimentation, and destruction of riparian vegetation threaten what remains. Little is known about the extent and distribution of invasive exotic species in the Tomales Bay watershed.

Action 4.0

Promote and support public outreach and education about Tomales Bay and its watershed: The Tomales Bay watershed comprises a diverse community of private and public landowners, villages and residents from the slopes of Mount Tamalpais to the town of Tomales and eastward to Chileno Valley. An engaging public outreach and educational program directed at residents and visitors to the watershed will be essential to the reduction of the impacts of ever-intensifying patterns of use.

Further detail for each action is provided within the respective sections of the Plan, and includes: prioritized projects, studies, and programs complete with preliminary budget estimates, time lines and potential lead and partner agency(s) and/or organization(s). In this manner, the public and members of the Council can use this Plan either collectively or individually for direction on the development and implementation of watershed stewardship activities. In addition to supporting such activities through the actions, this Plan provides indepth background information and a literature review for water quality, and erosion and sedimentation, and a glossary of watershed terms within respective appendices. The extensive work needed requires the support and participation of residents and the communities in West Marin. The Council provides a venue for the expression of concerns and ideas for the collective management of the watershed and supports any effort to achieve the Plan goals.

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List of acronyms and abbreviations used in this Plan: ACR – Audubon Canyon Ranch, Cypress Grove Research Center Basin Plan – RWQCB Water Quality Control Plan BMP – Best Management Practices BRIE - Biogeochemical Reactions in Estuaries CalTrans – State of California Department of Transportation CCC – State of California Coastal Commission CDHS – State of California Department of Health Services CDFG - State of California Department of Fish and Game Council – Tomales Bay Watershed Council CWA – Clean Water Act CWC – California Water Code EAC – Environmental Action Committee of West Marin EHS - Marin County Department of Environmental Health Services EQIP – Environmental Quality Incentives Program ESA – Endangered Species Act FDA – U.S. Food and Drug Administration GFNMS – Gulf of the Farallones National Marine Sanctuary GGNRA – Golden Gate National Recreation Area GIS – Geographic Information Systems JARPA- Joint Aquatic Resources Permit Application LMER - Land Margin Ecosystem Research MALT – Marin Agricultural Land Trust MCDHHS – Marin County Department of Health and Human Services MRCD – Marin Resource Conservation District MCSTOPPP – Marin County Stormwater Pollution Prevention Program MMWD – Marin Municipal Water District NGO – Non-governmental organization NOAA – National Oceanic and Atmospheric Administration NMWD – North Marin Water District NPS - National Park Service NRCS – Natural Resources Conservation Service NSSP – National Shellfish Sanitation Program OSDS – Onsite Sewage Disposal System PRBO – PRBO Conservation Science PRNS - Point Reyes National Seashore QA/QC – Quality assurance /Quality control RCD – Resource Conservation District RWQCB - Regional Water Quality Control Board/San Francisco Regional Water Quality Control Board SCS – Soil Conservation Service SFRWQCB - Regional Water Quality Control Board/San Francisco Regional Water Quality Control Board SFSU – San Francisco State University SPAWN – Salmon Protection and Watershed Network Tomales Bay Watershed Stewardship Plan: A Framework for Action 5

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STRAW - Students and Teachers Restoring A Watershed SUSD – Shoreline Unified School District SWQCB - State Water Quality Control Board TAC - Technical Advisory Committee TBA- Tomales Bay Association TBAG – Tomales Bay Agriculture Group TBSTAC – Tomales Bay Shellfish Technical Advisory Committee TBWC- Tomales Bay Watershed Council TMDL – Total Maximum Daily Loads TSS – Total Suspended Sediments UCCE – University of California Cooperative Extension UC –University of California UCD – University of California at Davis USACE – U.S. Army Corps of Engineers USCG – U.S. Coast Guard USDA – U.S. Department of Agriculture USDA-CREP – Conservation Reserve and Enhancement Program USEPA – U.S. Environmental Protection Agency USFWS – U.S. Fish and Wildlife Service USGS – U.S. Geological Survey WDR – Waste Discharge Requirements WMS – Waste Management Systems WQS – Water Quality Standard

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INTRODUCTION

The Tomales Bay watershed is remarkable for its beauty and its diversity of wildlife. It is home to nearly forty species of land mammals including bobcat, mountain lions, and coyote; marine mammals; river otters; and hundreds of species of birds. Nearly half the bird species of North America have been spotted in this region. It also provides sanctuary to 26 federally protected species, notably remnant populations of coho salmon and steelhead trout. During the last two centuries, the watershed’s rich natural resource base has sustained a local agricultural community, mariculture industry, and commercial and recreational fisheries that have provided high quality products both locally and to the San Francisco Bay Area and beyond. Today, the region has a resident population of approximately 11,000 people, mostly clustered in eleven villages, as well as more than 2.5 million visitors annually. Past and present human activities in the Bay and watershed have had significant cumulative impacts on water quality, habitats and species, resulting in a need for comprehensive watershed management. Among the activities that have affected the watershed are: residential development with its associated septic and other infrastructural needs, roads, agriculture, shellfish harvesting, forestry, recreation, mining, water impoundments and the creation of large-scale reservoirs. In order to protect and restore the health and vibrancy of the bay and watershed, local communities and landowners have joined public agencies and conservation organizations to form the Tomales Bay Watershed Council (Council) to develop this Watershed Stewardship Plan (Plan) that addresses key problems. The purpose of this Plan is to address human activities that affect water quality and habitats in Tomales Bay and its watershed, and management needs in ways that recognize and support beneficial watershed activities. These beneficial activities include wildlife habitat, agriculture, commercial shellfish harvesting, commercial and sport fishing, and recreation. Past accomplishments that preceded the creation of this Plan and support needed future action include: the preservation and protection of open space and agricultural lands, implementation of soil and water conservation projects, restoration of aquatic habitat, restoration of aquatic and riparian habitats, and the prohibition of jet ski use in the bay and its tributaries. More specifically, the goals of this Watershed Stewardship Plan are to: Ensure water quality in Tomales Bay and tributary streams sufficient to support natural resources and sustain beneficial uses. Restore and preserve the integrity of natural habitats and native communities. Develop strategies to implement the Plan and to protect the watershed.

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This Plan contains recommendations to accomplish each identified watershed goal, and a literature review by subject area (see appendices) as a blueprint to guide future actions. Both summary information and additional detail is provided in the appendices to improve our collective understanding of watershed issues, trends and future management and conservation needs. The Council will support implementation of the Action Plan by local organizations and agencies, and undertake specific projects that are beyond the jurisdiction and/or mandate of any single watershed partner or existing partnerships. This Plan is intended to provide a tool for public outreach and education to solicit the involvement of citizens, landowners and agencies with jurisdiction and management responsibility in the Tomales Bay watershed. Past accomplishments of local organizations, landowners and agencies will provide a strong foundation in accomplishing these goals. As the Action Plan is implemented, additional information will be collected, and these new reports and amendments will be incorporated into the Plan.

1.0 Tomales Bay Watershed Council Formation and Vision The formation of the Tomales Bay Watershed Council and the development of the Tomales Bay Watershed Stewardship Plan was somewhat anticipated at the second State of Tomales Bay Conference (1990) when Senator Peter Behr made the following statement: "…We have sought consensus. We have emphasized local concerns and problems which threaten the health of the Bay. We need scientific research as a bedrock - foundation for this management plan to grow up and rise…Whatever plans we arrive at, for the sake of a holistic approach, we must look down on the Bay like an eagle overhead, observing all of its various parts and how they interlock…" In 1999, the Tomales Bay Advisory Committee led community members in identifying the critical need for a locally based, coordinated watershed management effort. After consultation with agencies and local organizations, the Council was convened in January of 2000 to develop a plan to improve the water quality of Tomales Bay and tributary streams, and to protect and restore the entire watershed in a manner that sustains human and natural resources. The Tomales Bay watershed includes a number of communities, diverse local interest groups and organizations, and falls into the jurisdiction of many local, state and federal agencies. Many of these entities are already involved in efforts to protect and improve the health of the watershed either individually or through partnerships with others. The Tomales Bay Watershed Council (Council) is currently the only organization considering issues facing the future of the Tomales Bay watershed in which all stakeholders participate. The Council’s 24 members are drawn from local interest groups and agencies affected by or responsible for the watershed. The aim is to provide a continuing, collaborative forum to improve our capacity to comprehensively manage and protect Tomales Bay and its watershed and the interests of stakeholders. The Council has a broad-based membership representing Tomales Bay Watershed Stewardship Plan: A Framework for Action 8

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most stakeholders in the watershed, including: 1) residential and community groups, 2) agricultural interests, 3) environmental groups, 4) maricultural interests, 5) recreational interests and 6) public agencies. At the inception of the Council, members agreed on the following common interests: to protect the Tomales Bay ecosystem; to maintain the rural nature and quality of life within the watershed; to use a collaborative approach to sustain agriculture, mariculture, homeowners, recreation and natural resources; and to strike the appropriate balance between voluntary and regulatory efforts. The Council recognizes that there are two underlying issues facing the future of the bay and watershed, namely: the effective and economical management of all the sources of pollution that may impact the bay ecosystem, and the growing human pressures on this ecosystem. With these interests and issues in mind, the Council has committed to a vision for the watershed where: • human activities in the watershed -including agriculture, recreation, commercial fishing, and residential use - coexist with high, sustainable or improving levels of ecosystem health and watershed function; • natural habitats and a broad diversity of wildlife species, including salmonid populations, are restored throughout the watershed; • water quality of the bay and its tributaries meets state standards for shellfish mariculture (as a benchmark for clean water); • sustainable agriculture is one of the primary land uses in the watershed; • the rural character and quality of life for local residents and communities is preserved; and • the public participates in planning and managing the watershed.

2.0 Past Accomplishments in the Tomales Bay Watershed “In my view, Marin can – and should – serve the rest of the nation as an example of how intelligent voting, careful planning, environmental education, and volunteer stewardship can protect our most vital resources.” -- Dr. Martin Griffin, Saving the Marin-Sonoma Coast, Sweetwater Springs Press, 1998

Tomales Bay and its surrounding watershed support an extraordinary and diverse ecosystem that is the product of the natural geology, hydrology, and the Mediterranean climate of the region. Vast open spaces that remain across private lands in the watershed have contributed to a level of watershed health and function that would have been lost if stable agricultural property ownership, local communities and organizations, agencies and county policies were not working together to preserve this character during the last 30 years. In addition, the creation of the Point Reyes National Seashore, and state and county parks have preserved the natural condition and biodiversity in much of the watershed. This legacy of open space and preservation is the result of both collaboration and confrontation, and provides an important Tomales Bay Watershed Stewardship Plan: A Framework for Action 9

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foundation that will support needed future action to protect and enhance the environment and water quality of the Tomales Bay watershed. This legacy also demonstrates the collective and individual capacity of local, state and federal organizations to continue this work in the future. Despite decades of individual efforts to improve the watershed, significant problems remain. The following examples are not intended to provide a comprehensive accounting, but merely to highlight the variety of projects, programs and policies that have been realized locally, and the broad spectrum of actions that can be anticipated in the future. •

Past accomplishments in the Tomales Bay watershed by Audubon Canyon Ranch (ACR) include: acquisition, protection and management of approximately 450 acres of shoreline properties; restoration of salt and freshwater marshes; restoration of coastal prairie; beach cleanups; survey and removal activities to control exotic pest plants; inventorying and monitoring bird populations and rare salt marsh plants; ongoing natural history educational programs; and numerous scientific ecological studies.

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The California Department of Fish and Game’s (CDFG) Fisheries Restoration Grant Program has contributed $700,000 towards planning, assessment, and restoration projects within the Tomales Bay watershed during the last five years. This funding has produced the Walker Creek Watershed Plan and subsequent riparian fencing, revegetation, alternative water source and erosion control implementation projects in partnership with the Marin RCD; sediment source reduction in the Lagunitas Creek watershed in partnership with the Marin County Open Space and Marin Municipal Water Districts; riparian fencing in Lagunitas Creek watershed in partnership with the Tomales Bay Association and National Park Service; riparian enhancement in Lagunitas Creek watershed in partnership with Marin Municipal Water District; and salmon and steelhead trout monitoring in Lagunitas Creek watershed in partnership with the National Park Service. Most recently, CDFG has funded the Tomales Bay Watershed Council to continue its outreach, education, and watershed planning and assessment efforts.

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The California State Coastal Conservancy (Conservancy) has been actively participating in conservation and restoration efforts in Tomales Bay for over 25 years. Working with partners such as MALT, the Marin RCD, NPS and Marin County, the Conservancy continues to fund projects to restore and enhance the agricultural and natural resource values of West Marin. The Conservancy has been an active participant in watershed planning in Tomales Bay since the early eighties, and is one of the contributors funding this plan. Other Conservancy projects have included acquisitions of agricultural and conservation easements throughout the watershed, erosion control, livestock fencing and stream revegetation projects, an assessment of fish passage barriers in Marin County, and an assessment of on-site septic systems and their impact on coastal waters.

•

Past accomplishments of California State Parks include: development of a General Plan that addresses Tomales Bay water quality, resource management, and land

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acquisition; water quality monitoring; on-going erosion control projects; and maintenance of all facilities at Samuel P. Taylor, Tomales and Millerton State Parks. •

During the last three decades, the County of Marin (County) has increased minimum parcel size in agriculturally zoned lands from 5 to 60 acres, and has provide increasing protection for riparian areas and fisheries through the Countywide Plan, and creek and grading ordinances. These policies were the subject of review in 1997 when FishNet 4C was formed to focus on improving county practices and policies affecting fisheries, and resulted in the formation of a Marin County fishery protection team. The County has also created a training program for county road maintenance, and a program to address fish barriers. In 2002, the County actively endorsed the Streamside Conservation Area ordinance on all undeveloped parcels adjacent to blue line streams. The County has acquired land for three active parks, and the Marin County Open Space District has acquired over 2000 acres for passive recreation. In partnership with the East Shore Planning Group, the County has received $600,000 in funding for water quality studies and related research to improve wastewater treatment and failing septic systems. The County has provided $50,000 annually to the Marin Resource Conservation District and $50,000 to date to the Council to support their recognized benefits to the bay; in addition to lobbying for the Pacific Coastal Salmon Recovery Initiative, which to date has provided $1 million to projects in the Tomales Bay Watershed.

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Since its inception in 1970, the Environmental Action Committee of West Marin (EAC) has successfully fought a number of proposed developments including the diking of the southern end of Tomales Bay for agriculture. EAC has successfully challenged Marin County approvals of numerous developments that would have intruded into stream and wetland buffer zones, and has worked with the County to improve its enforcement of existing stream and wetland protections. EAC won its five-year campaign to ban jet skis from Tomales Bay and the GFNMS, which is now the largest jet ski-free area in the United States. In coalition with other local groups, EAC stopped the West Marin landfill from expanding. EAC published the first regional Green Guide on recycling, reuse, and reduction of waste and co-produced all four State-of-the-Bay conferences.

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Past accomplishments in Tomales Bay by the Gulf of the Farallones National Marine Sanctuary (GFNMS) include: preventing construction on the sea bed; preventing dredging; assisting marine and National Park Service (NPS) regulators with water quality enforcement; banning jet skis; providing funding for riparian restoration projects; assisting with the removal of the Giacomini Dam in 1990; and protection of harbor seal haul-outs within the Bay.

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Kayaking companies permitted to operate on Tomales Bay have worked with the PRNS to implement a program to educate visitors about toilet facilities; and require overnight camping kayakers to travel with the means to carry out human waste. To meet this objective these companies rent port-a-potties to overnight kayak renters, and provide waste facilities on day tours as needed. Tomales Bay Watershed Stewardship Plan: A Framework for Action 11

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The Marin Agricultural Land Trust (MALT) is a nonprofit community-based organization created in 1980 to help protect and preserve Marin County agricultural lands for agricultural use. As of December 2002, MALT held conservation easements 26,000 acres in the Tomales Bay watershed. These lands are economically productive and environmentally important which MALT has permanently protected from subdivision and non-agricultural development. MALT easements also prohibit uses or activities that would result in significant soil degradation or significant pollution of surface or subsurface waters.

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Since 1959, the Marin Resource Conservation District (MRCD) has endeavored to conserve and enhance the watershed’s natural resources, including soil, water, vegetation and wildlife while maintaining a viable agricultural economy. Over 100 conservation projects have been completed to this end, including gully repairs, streambank stabilization, road repairs and manure management projects. Repairs have also included the installation of native riparian vegetation, livestock fencing, water troughs, livestock crossings, check dams, headcut repairs, sediment retention ponds, culverts, dairy methane digestion, soil aeration and no-till drillage. Over 3.5 million dollars have been spent on such projects - in addition to critical watershed planning, studies and assessment work- to improve water quality, aquatic and terrestrial wildlife habitats. Monitoring results have documented restoration of riparian habitats and increases in neotropical songbird use on some agricultural lands. Currently, ranchers in the Walker Creek subwatershed are nearing completion of 6 contiguous miles of stream restoration. In the next three years, the MRCD will be administering 2 million dollars to continue conservation efforts in the Tomales Bay watershed.

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The U.S. Department of Agriculture Natural Resource Conservation Service (USDA NRCS) has provided technical and financial assistance through the Environmental Quality Incentives Program (EQIP) to 18 agricultural property owners in the Tomales Bay watershed. This assistance included $450,316 to implement water quality Best Management Practices (BMPs). The agricultural producers agreed to pay an in-kind contribution of more than $200,000 for the EQIP money awarded. Practices included: riparian fencing, livestock crossings, and off-stream water development for riparian area protection; manure holding ponds and fresh water diversions were constructed for improved dairy manure management; and crossfencing and livestock water facilities were installed for improving livestock grazing management.

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The Point Reyes National Seashore (PRNS) has a long-term interest in the health of Tomales Bay, and to guide its actions and promote coordination with other agencies, developed the Tomales Bay: Guidelines for Protection and Use (2001). In addition, PRNS has secured funding for riparian protection fencing along Olema Creek, initiated a planning process for the restoration of wetlands at the southern end of the bay, established a water quality monitoring program, and developed an education and camping permit system for users of this important estuary. PRNS law enforcement staff also provide search and rescue functions on the bay throughout the year. To Tomales Bay Watershed Stewardship Plan: A Framework for Action 12

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enhance coho salmon and steelhead trout populations, PRNS has conducted several projects to remove fish passage barriers on Olema Creek and its tributaries. •

The San Francisco Bay Regional Water Quality Control Board (RWQCB) formed and facilitates the Tomales Bay Shellfish Technical Advisory Committee (TBSTAC). This committee brings agencies and local stakeholders together to form and implement recommendations and has provided an impetus for the creation of the TBAG, a recent septic evaluation and improvement program undertaken by the East Shore Planning Group, and the Council. The RWQCB has been the driving force behind remediation and monitoring of mercury from the Gambonini mine in the bay and tributaries, and has recently completed a draft pathogen Total Maximum Daily Load (TMDL) report identifying pathogen sources. The RWQCB has administered considerable funding for projects ranging from erosion control to septic improvements; and in the more distant past, the RWQCB instituted regulations on discharges into Tomales Bay, put all treatment plants in the watershed under permits, and required improvements on dairy facilities.

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The Tomales Bay Agriculture Group (TBAG) members, in collaboration with the Marin RCD and Natural Resource Conservation Service, are working to protect and restore riparian and stream resources on ranches and dairies. TBAG members cooperate with University of California Tomales Bay Water Quality Project to implement water quality improvement practices and to monitor their effectiveness. Water quality data is being collected from loading units that represent land use practices within these facilities. This project is identifying and prioritizing areas and practices that can reduce bacteria, nutrient, and sediment loading from Bay tributary watersheds. Recently four of the study cooperators received letters of recognition from the San Francisco Regional Water Quality Control Board for their efforts to improve water quality.

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The Tomales Bay Association (TBA) has conducted a salmonid monitoring and restoration program since 1986 on Olema Creek. TBA installed livestock exclusion fencing and planted thousands of willows to improve riparian habitat. TBA has also assisted the NPS with other fencing projects on Cheda and Devil’s Gulch streams, and has published numerous educational documents. TBA was a major participant in the State Water Resources Control Board (SWRCB) Hearings which culminated in the 1995 SWRCB Order 95-17 to protect coho salmon, steelhead and other aquatic species in Lagunitas Creek; and TBA recently negotiated, with invaluable assistance from Trout Unlimited, a settlement agreement with North Marin Water District establishing a precedent-setting, first-time dedication of appropriative water rights for instream habitat purposes.

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The University of California Cooperative Extension (UCCE), Sea Grant has initiated a pilot program to restore native oysters in Tomales Bay. The project is designed to provide complex habitat that will be colonized by Olympia oysters and ultimately serve as habitat for numerous fish and invertebrates. The project is being

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conducted in cooperation with researchers at UC Davis and San Francisco State University (SFSU) in collaboration with NOAA Fisheries.

3.0 Federal, State and Local Watershed Conservation Legislation State policy for water quality control in California is directed toward achieving the highest water quality consistent with maximum benefit to the people of the state. According to this policy and the requirements of the 1972 Clean Water Act (CWA) and federal, state and local legislation, beneficial uses have been identified for waterbodies in California. Under Section 303(d) of the CWA, states, territories and authorized tribes are required to develop a list of water quality limited waterbodies that do not meet water quality standards, even after point sources of pollution have installed the minimum required levels of pollution control technology. The law requires that these jurisdictions establish priority rankings for these waterbodies, and then develop action plans, called TMDLs, to improve water quality. By law, the RWQCB is required to develop, adopt and implement a Water Quality Control Plan (Basin Plan) for the San Francisco Bay region, which includes Tomales Bay watershed (for additional information go to: http://www.swrcb.ca.gov/rwqcb2/). The Basin Plan is the master policy document that contains descriptions of the legal, technical, and programmatic bases of water quality regulation in the San Francisco Bay region. The beneficial uses described in the Basin Plan (California Regional Water Quality Control Board, 1995) define the resources, services and qualities of aquatic systems that are the water quality goals of protecting and achieving high water quality within the basin. Beneficial uses serve as a basis for establishing water quality objectives and discharge prohibitions to attain this goal and generally apply to all tributaries of a waterbody (including groundwaters, marshes, and mudflats in addition to the surface waters within a watershed). The Basin Plan's list of beneficial uses is not exclusive, and therefore beneficial uses which are not listed, but do exist, are also protected. In addition to these legally recognized beneficial uses, there are additional uses of waters in the Tomales Bay watershed that humans depend on and enjoy the benefit of (e.g. surface water in the Lagunitas Creek watershed is collected for water supply to Marin County). If a waterbody exceeds the maximum allowable pollution levels or fails to meet a recognized designated beneficial use, it is deemed “impaired” and a TMDL must be developed to addresses the causes of impairment, sources of pollution, and necessary actions to restore the waterbody. Tomales Bay’s designated beneficial uses as listed by the RWQCB's Basin Plan include wildlife habitat, preservation of rare and endangered species, marine habitat, fish migration, fish spawning, water contact recreation (swimming, boating, etc.), non-water contact recreation (hiking, bird-watching, picnicking), commercial and sport fishing (halibut, clams, herring, rock crab, and ghost shrimp), and commercial aquaculture of shellfish (California Regional Water Quality Control Board, 1995). The beneficial uses recognized for Lagunitas Creek are: cold freshwater habitat, preservation of rare or endangered species, fish migration and spawning, wildlife habitat, swimming, and agricultural water supply (California Regional Water Quality Control Board, 1995). Walker Creek’s recognized beneficial uses Tomales Bay Watershed Stewardship Plan: A Framework for Action 14

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are: cold freshwater habitat, preservation of rare or endangered species, fish migration and spawning, and wildlife habitat. Tomales Bay, Lagunitas and Walker creeks have all been designated as impaired bodies of water by the San Francisco Bay RWQCB due to excessive sedimentation, nutrient levels, pathogens and metals (mercury) and are officially listed on the federal 303(d) list of impaired waterbodies. Under the CWA, pollution is defined as human created or induced alteration of the physical, biological, and chemical character of water, thereby producing undesirable environmental effects. The RWQCB is currently working to identify pollutant-loading sources for these parameters, and to allocate amounts for each loading source to meet the goals in the Basin Plan. Subsequently, they will then develop an implementation plan to meet the allocated amount for each source, and to ultimately restore beneficial uses. In November 2002, the Tomales Bay pathogen sources and loading report and the draft implementation plan was issued, and TMDLs will be developed for the remaining sources of impairment in the next 3-5 years with a final completion date of 2007 (California Regional Water Quality Control Board, 1995). Each step in this process will include relevant stakeholder groups in the refinement and implementation of these action plans, and the RWQCB has adopted a watershed approach to addressing the sources of impairment. In addition to the Clean Water Act, there are numerous laws applicable to watershed conservation and management. Some of the laws and ordinances applicable to Tomales Bay watershed conservation and management are described below, however this is not a comprehensive list and all projects with potential environmental impacts must include environmental review and permitting in their planning. 3.1 Federal laws Endangered Species Act, 1973 (ESA). Lead Agencies – U.S. Fish and Wildlife Service (USFWS) for inland habitats, NOAA Fisheries (NMFS) for coastal and marine habitats. The ESA prohibits any person from “taking” endangered or threatened species. This act requires federal agencies to ensure that any action does not jeopardize the continued existence of any endangered or threatened species or result in damages to the species’ habitat. Marine Protection, Research, and Sanctuaries Act, 1972. Lead Agencies – NOAA/Gulf of the Farallones National Marine Sanctuary, National Parks. This Act recognizes “Certain areas of the marine environment possess(ing) conservation, recreational, ecological, historical, scientific, educational, cultural, archeological, or esthetic qualities which give them special national, and in some cases international, significance.” Specifically this law intends to “Improve the conservation, understanding, management, and wise and sustainable use of marine resources; (to) enhance public awareness, understanding, and appreciation of the marine environment; and (to) maintain for future generations the habitat, and ecological services, of the natural assemblage of living resources that inhabit these areas.”

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Agricultural Improvement and Reform Act (Farm Bill). Lead Agency – U.S. Department of Agriculture (USDA). This act provides incentives to American agricultural communities to promote conservation and land improvement practices to protect the surrounding environment. Financial incentive programs are administered by the Natural Resource Conservation Service (NRCS). National Environmental Policy Act, 1969. Lead Agencies – all federal agencies. NEPA is the foundation for national environmental protection. It requires review of all major federal activities that may cause adverse environmental impacts. Coastal Zone Management Act (CZMA) and Reauthorization Amendments (CZARA). Lead Agencies – National Oceanic and Atmospheric Administration (NOAA); U.S. EPA Cooperating State Agencies – State Water Quality Control Board; California Coastal Commission. The CZMA provides some control to states to protect coastal resources that may be negatively affected by activities occurring in federal waters. In addition, the CZARA requires states to implement Coastal Nonpoint Pollution Control Programs. 3.2 State laws California Environmental Quality Act (CEQA). Lead Agencies – all state agencies. The overall goal of CEQA is to develop and maintain California’s environment with the specific goals of requiring all state and local agencies to identify the significant environmental effects of their actions; and either avoid those significant environmental effects, or mitigate those significant environmental effects, where feasible. This process provides the public with detailed information on the potentially significant environmental effects which a proposed project is likely to have and to list ways which the significant environmental effects may be minimized and indicate alternatives to the project. State Coastal Act, 1976. Lead Agency – California Coastal Commission; Cooperating Agencies – all counties. Requires all counties to preserve and protect coastal waters by developing a local coastal plan (LCP). Porter-Cologne Water Quality Control Act. Lead Agencies - State Water Quality Control Boards; Regional Water Quality Control Boards. California’s primary water law, this act provides a coordinated framework for waste discharges to all surface and ground water in the state. It requires the development of regional water quality control plans (Basin Plans) throughout the state, which must include: beneficial uses which are to be protected; water quality objectives which protect those uses; and an implementation plan to accomplish those objectives. This act includes Waste Discharge Requirements (WDR), which regulate all point and nonpoint discharge of pollutants that could impact water quality or beneficial uses. In addition, it requires two additional components to the TMDL not required by the CWA: an implementation plan and monitoring plan.

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California Fish and Game Regulations. Lead Agency – Department of Fish and Game (DFG). The state code which regulates sport and commercial fishing activities, mariculture, hunting and harvesting of wild plants and animals. California Endangered Species Act (CESA). Lead Agencies - all state agencies are required to consult with the Department of Fish and Game (DFG) to ensure that any action it undertakes is not likely to jeopardize the continued existence of any endangered or threatened species or result in destruction or adverse modification of essential habitat. CESA generally parallels the main provisions of the Federal Endangered Species Act and is administered by DFG. Under CESA the term “endangered species” is defined as a species of plant, fish, or wildlife which is “in serious danger of becoming extinct throughout all, or a significant portion of its range” and is limited to species or subspecies native to California. CESA prohibits the "taking" of listed species except as otherwise provided in State law. Unlike its Federal counterpart, CESA applies the take prohibitions to species petitioned for listing (state candidates). §86 of the Fish and Game Code defines “take” as “hunt, pursue, catch, capture, or kill, or attempt to hunt, pursue, catch, capture, or kill.” The Natural Community Conservation Planning Act (NCCP Act) was added to CESA in 1991. (Fish & Game Code §§2800-2840). These provisions provide for voluntary cooperation among DFG, landowners, and other interested parties to develop natural community conservation plans which provide for early coordination of efforts to protect listed species or species that are not yet listed. The primary purpose of the NCCP Act is to preserve species and their habitats, while allowing reasonable and appropriate development to occur on affected lands. California Riparian Habitat Conservation Act. Lead Agency – Department of Fish and Game (DFG). The purpose of this act is to protect, preserve and restore riparian habitats throughout the state. This program purchases land for preservation and restoration. Streambed Alteration Agreement. Lead Agency – Department of Fish and Game (DFG). Under this agreement, the DFG regulates activities such as grading, filling, dredging that occur in streams and rivers. The DFG provides guidelines to implement best management practices to avoid adverse impacts to riparian areas, streams and rivers. Salmon, Steelhead, Trout, and Anadromous Fisheries Program Act. Lead Agency – Department of Fish and Game (DFG). This act necessitates the protection of anadromous fish species throughout the state, and improvement of stream habitat to increase natural spawning potential. 3.3 County laws Marin Local Coastal Program, 1980 (LCP). Lead Agency – County of Marin, Cooperating State Agency – California Coastal Commission. The primary goal of the LCP is to ensure that the local government's land use plans, zoning ordinances, zoning district maps, and implemented actions meet the provisions and polices of the Coastal Act at the local level.

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Countywide Plan (General Plan), 1994. Lead Agency – County of Marin. The Marin Countywide Plan is the County's long-range guide for land use and protection of natural resources. The Plan provides specific policy direction for land in unincorporated areas and general guidelines for the cities and towns of Marin. It provides policies and programs for the public, planning staff, and decision makers when reviewing and analyzing proposed development.

4.0 Watershed Conservation and Stewardship “Tomales Bay is the perfect place for us to demonstrate good watershed citizenship: it belongs to a large system of coastal estuaries but is small enough for us to take care of. Our stewardship can be a model, but to succeed, will take all of us working together.” -- Don Neubacher, National Park Service

A watershed encompasses the entire area that drains into a creek, river or bay. The term watershed is used interchangeably with the terms catchment area and drainage basin. Large watersheds have smaller sub-watersheds within them. Tomales Bay’s watershed includes those of Lagunitas and Walker creeks, as well as the smaller tributaries that flow directly into the estuary. The health of creeks, lakes, estuaries and bays is a consequence of the hydrologic cycle (the passage of water from the oceans into the atmosphere, onto the land, over and under the land as run-off and infiltration, and back into the oceans) and human and natural processes at work on a watershed’s land area. The character of each watershed (its wildlife, vegetation, and habitats) varies according to its location, geology, human influences, and other factors. Every person lives within a watershed. All of our actions - including hiking, driving on paved or dirt roads, building homes, raising livestock, gardening, boating, drinking water, or enjoying the benefits of indoor plumbing - affect the watershed in which these activities occur. As a resident or landowner within a watershed, each individual is responsible for being an informed watershed citizen who responsibly manages his/her impacts, while supporting conservation of the larger system. A watershed is a series of interconnected ecosystems that interact in a dynamic manner. The understanding and recognition of these respective ecosystems will improve our capacity to manage potential impacts. These diverse ecosystems include: •

Upland areas. Uplands in the Tomales Bay watershed include coniferous and hardwood forests, coastal scrub communities, grasslands, and shrub dominated ecosystems. These ecosystems play a critical role in the cycling of water by intercepting, storing and utilizing a large amount of the precipitation that falls within a watershed. Healthy uplands also provide diverse habitats for wildlife, air purification, and recreational values for humans.

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Riparian communities. Riparian communities include the streamside vegetation and associated organisms situated alongside creeks or rivers. When these creekside areas are subject to periodic flooding and sediment deposition, they are called floodplains. Riparian areas are critically important for economic and ecological reasons that include: maintenance of water quality and the aquatic ecosystem, erosion control, flood dissipation and water storage, groundwater recharge, nutrient cycling, wildlife and fisheries habitat for many sensitive species, biological diversity, migration corridors, agricultural and ranching activities, and human enjoyment. The importance of riparian areas is out of proportion to the relatively minor area of land they occupy in most watersheds. Increasingly, efforts are being made to protect these areas from degradation caused by human activities.

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Wetlands. Generally, wetlands are lands where saturation with water (fresh or salt) is the dominant factor determining the nature of soil development and the types of plant and animal communities living in the soil and on its surface. Much of the planet's life depends on the existence of wetlands. They are vital to the survival of many fish and other aquatic life forms, birds, and plants. They filter and clean water, prevent soil erosion, and provide flood control among numerous other benefits. Even as appreciation for the benefits provided by wetlands has grown over the last couple of decades, wetlands continue to be filled, drained, and dredged. California today has only 10 percent of the wetlands that existed before settlement by Europeans. Only 5 percent of the state's coastal wetlands remain intact. Government efforts in response to these losses have come in the form of legal restrictions on uses of wetlands as well as protection through acquisition, restoration, and management. While these approaches have done a great deal to preserve wetlands and prevent their indiscriminate destruction, they cannot reach all wetlands. The lands with the greatest potential for wetland restoration and management are mostly in private ownership, and as a result landowners have the opportunity to play a significant stewardship role.

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Waterbodies and Aquatic Ecosystems. These are comprised of living and nonliving components that include surface and groundwater, plants, fish, mammals, invertebrates and other aquatic insects, benthic organisms, amphibians, and bed material or substrate. Their water quality is the product not merely of the nature and quantity of the chemicals in its waterbodies, but also of its climate, geology, soils, geomorphology, vegetation, adjacent land-use and various human activities. o Streams. Streams are dynamic, changing systems. The slope, shape and material of a streambed develop to accommodate the typical pattern of its stream flows. Steams also respond to changes in bank vegetation and in water delivery, as well as to adjacent human activities. If the rate or amount of water delivered to the system as overland flow is increased and natural stream balance is lost, streams can over-widen, down-cut their channel bottom, and cut into their banks as they re-establish equilibrium. Human activities that can result in stream erosion include development, paving, forest and riparian community removal or diminution, and soil compaction. Reducing streamflow can lead to many changes in an aquatic system, and die-off of adjacent Tomales Bay Watershed Stewardship Plan: A Framework for Action 19

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vegetation. Streams have a natural tendency to move within their floodplains, often flowing through multiple channels, or switching from one mainstem to another over the years. This lateral movement is a natural part of stream behavior and serves to restore a broad floodplain. o The bay. Tomales Bay is an estuary in which freshwater mixes with salt water to create a unique set of habitats. An estuary is often referred to as a “zone of transition,” from land to sea and from fresh to salt water. Estuarine habitat types include shallow open waters; fresh, brackish and salt marshes; sandy beaches, tidal mud and sand flats; rocky shorelines; creek deltas and eelgrass beds. In California, estuaries have been referred to as the “ocean’s nursery” because these waters support the early life stages for many important organisms. Tomales Bay provides critical breeding and rearing habitat for many aquatic and marine species, both migratory and resident. Watershed stewardship must address these ecosystems and their dynamic interactions. Effective management understands, respects, and works with natural processes. Due to the complexity of these systems, watershed planning requires an inter-disciplinary, stakeholderbased process for natural resource management. During the last decade, watershed councils have been formed to address water quality problems and habitat restoration needs across the nation. In California and elsewhere, councils have been created to develop watershed-based strategies to protect habitats and open space, while promoting sustainable land-use practices and the health of coastal watersheds. The Tomales Bay Watershed Council was created for these very reasons.

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II. WATERSHED CHARACTERIZATION A. A DESCRIPTION OF THE TOMALES BAY WATERSHED This description reviews existing literature describing Tomales Bay and its watershed. This information is intended to provide a foundation from which the Stewardship Plan can draw. The emphasis here is on existing pertinent literature describing the physical, chemical and biological processes that have been studied. A more detailed presentation of this information and the conclusions that have been drawn is included in the appendices. This information is intended enable us to discern physical, chemical and biological trends in the watershed, to evaluate the need for future studies and assessments, to identify conservation and management requirements, and to understand the impact of human activities on Tomales Bay and its watershed.

1.0 General description The Tomales Bay watershed extends from Mount Tamalpais and Bolinas Ridge, east to the headwaters of Walker Creek and Nicasio and Lagunitas Creeks, and west to the Inverness Ridge (see Figure 1). The lands of the watershed include privately owned ranchlands, parklands, public water districts, and residential areas. The watershed is rugged with a maximum elevation of 794 meters (Mount Tamalpais) and several other peaks that exceed 300 meters. The watershed supports various plant communities, including Bishop pine forests, mixed evergreen forests of oak, Bay and Douglas fir, annual and perennial grasslands and rangelands, coastal strand and prairie, marshes and beaches and dunes (Shuford and Timossi, 1989; Evens, 1993). A diversity of marine habitats can also be found in the bay, including eelgrass beds, intertidal rocky shore, mud and tidal flats, streams and wetlands. Hundreds of species of mammals, birds, invertebrates and plants, and many threatened and endangered species inhabit the watershed, such as California freshwater shrimp, tidewater goby, coho salmon, steelhead trout, Pacific herring, California red-legged frog, western snowy plover, northern spotted owl, and the Point Reyes jumping mouse. The watershed is also an important foraging and haul out site for marine mammals and over-wintering area and a migratory stop along the Pacific Flyway for many species of birds, including approximately 20,000 shorebirds and 22,000-25,000 waterfowl (Kelly, 1992; Allen 1989). Humans and nature have co-existed in the Tomales Bay watershed since the earliest habitation by Coast Miwok, approximately 5,000 to 8,000 years ago. Uses of the watershed have significantly changed in the last 400 years since the arrival of first Mexican and then European settlers in the area. The watershed now supports a population of 11,000 in eleven villages, along with various economic enterprises including sheep and cattle ranching, dairying, farming, commercial fishing, oyster farming, and tourism. Tomales Bay Watershed Stewardship Plan: A Framework for Action 21

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Figure 1. The Tomales Bay watershed (map courtesy Point Reyes National Seashore). Tomales Bay Watershed Stewardship Plan: A Framework for Action 22

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Much of the western and southern portions of the watershed are under public ownership, and include parklands of the Point Reyes National Seashore, Golden Gate National Recreation Area (GGNRA), Tomales Bay State Park and Samuel P. Taylor State Park; as well as lands of the Marin Municipal Water District (MMWD), Inverness Public Utility District and Marin County and the Open Space District. Most of the eastern and northern areas are privately owned agricultural lands. Approximately 80 percent of the lands of the watershed (including private and public lands) are used primarily for agriculture as grazing lands for dairy and beef cattle and sheep (National Park Service, 2001). Villages and roads account for less than 1 percent of the land area. (National Park Service, 1995). 1.1

Summary of watershed reports and studies

A number of publications present issues at the watershed level, some of which identify relevant biological and ecological information, and strategies for conservation and project recommendations. These include: A Program for Restoring the Environment of Tomales Bay (California State Coastal Conservancy, 1984), the Marin Coastal Watershed Enhancement Project (University of California Cooperative Extension, 1995), the Lagunitas Creek Sediment and Riparian Management Plan (Prunuske Chatham, Inc., 1997); the Walker Creek Watershed Enhancement Plan (Prunuske Chatham, Inc., 2001); the Tomales Bay/Bodega Bay Watershed Boundary Study (National Park Service, 1995) and Tomales Bay: Guidelines for Management and Use (National Park Service, 2001). Also relevant is The Natural History of the Point Reyes Peninsula, since the eastern part of the Point Reyes Peninsula is in the Tomales Bay watershed (Evens, 1993). In 1995, the Point Reyes National Seashore Water Resources Management Plan, which contains relevant information on the Tomales Bay watershed was published (Bellinger, 1995). The Marin Countywide Plan and Local Coastal Program also provide information relevant to the watershed, as 50% of Marin County is within the Tomales Bay watershed (County of Marin, 1981). The Tomales Bay Environmental Study Compendium of Reports provides a broad spectrum of background information on the Tomales Bay watershed (Corwin, Ruthann, 1972). The earliest comprehensive study of the Lagunitas and Walker Creek watersheds, Master Drainage and Sediment Control Plan: Lagunitas and Walker Creek Watersheds (MCRCD, 1965), provides a basis of data for the watershed with a series of maps for rainfall, geology (sedimentary and intrusive), vegetation (three classes), urban areas, slope (three classes), and stream profiles for mainstem and tributaries with several channel cross sections. The Marin Coastal Watershed Enhancement Project (University of California Cooperative Extension, 1995) presents an overview of nonpoint source water quality issues associated with agriculture and natural resources in West Marin featuring Walker Creek as one of three watersheds profiled in detail. This report describes land use history, research, and restoration in these watersheds.

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2.0 Special Recognition of Tomales Bay “On the flood tide of a dark moon night in February, herring swarm into Tomales Bay, spawning amidst the eelgrass beds that line the calm shallows. The birds are waiting, mysteriously cued into the bounteous spawn. Scoters gather by the tens of thousands; bufflehead, ruddy duck, scaups, and grebes by the thousands; loons, brant, cormorants, pintail by the hundreds.” -- Jules Evens, The Natural History of the Point Reyes Peninsula, Point Reyes National Seashore Association, 1993

Tomales Bay has long been recognized as a special place deserving a high level of protection by citizens and local, state and federal agencies. Most of the bay and its shoreline were included in the National Park System through the creation of the PRNS in 1962 and GGNRA 1972. In 1979 the Regional Coastal Commission adopted a resolution designating Tomales Bay as a “Special Resource Area.” The designation covers “the coastal waters and immediately adjacent uplands of Tomales Bay” and was made “to denote the Commission’s commitment to the protection, enhancement, and where feasible, restoration of the unique and important natural resources of this area” (University of California Cooperative Extension, 1995). In 1981, the Bay became a part of the GFNMS, one of three such marine sanctuaries in the state. The bay is also part of the Central California Coastal Biosphere Reserve. Because of large numbers of wintering and migrating shorebirds, Tomales Bay qualifies for inclusion as a wetland of regional importance under the Western Hemisphere Shorebird Reserve Network (Kelly, 2001). In 2002, the US Fish and Wildlife Service (USFWS) included Tomales Bay as a "Wetland of International Importance" under an international treaty called the Convention on Wetlands (commonly known as the Ramsar Convention).

3.0 Physical Description 3.1 Tomales Bay Tomales Bay proper is a 28 km2 shallow, highly unidirectional, Mediterranean-type, coastal estuary. The bay alternates between a classical estuary (net dilutive basin) during wet winter months, and a hypersaline estuary (net evaporative basin) during dry summer months. Tomales Bay opens at the southern end of Bodega Bay and extends in a southeasterly direction. The bay is approximately 12 miles long and less than one mile wide (California Regional Water Quality Control Board, 2001). The average depth of the bay is less than 20 feet (State of California Department of Health Services, 2002). Tomales Bay hosts a diversity of habitats. The bay has intertidal, subtidal, and benthic habitats, as well as mud flats, and salt and freshwater marshes. Tomales Bay dunes, and their effects on tidal circulation and water depth at the mouth of the Bay, are noteworthy. These Tomales Bay Watershed Stewardship Plan: A Framework for Action 24

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dunes provide unique habitat; and the nearby tidalflats provide important habitats for many bivalve species, roosts and respite for birds and marine mammals. Large subtidal meadows of eelgrass grow in the northern half of Tomales Bay, between Pelican Point and Tom’s Point, where temperatures, salinities, and tidal exchange reflect those in the Pacific Ocean. This region of the bay is enriched by nutrients and plankton brought in by the tide from the ocean, as well as by the freshwater inflow and nutrients from Walker Creek (Smith and Hollibaugh, 1997; Hollibaugh et al., 1988). See attached appendices for additional information on water quality and sedimentation. 3.1.1 Freshwater inflow Water flow in the watershed has a significant effect on the habitats of the bay and its tributaries. Approximately 75 percent of the total inflow comes from Lagunitas and Walker Creeks (County of Marin, 1981). Six of MMWD’s reservoirs now capture about 40 percent of the freshwater that historically flowed into the Bay. The volume of freshwater inflow to Tomales Bay has been reduced still further by other tributary diversions (e.g., dams, water impoundments, irrigation systems, etc.) (National Park Service, 2001). Low freshwater flows can affect the bay in many ways, for example, by concentrating pollutants, thus diminishing water quality, and by degrading spawning and rearing habitat for salmonids and Pacific herring (University of California Cooperative Extension, 1995; Suer, 1987; National Park Service, 2001). Freshwater inflow reduces the bay’s salinity, and provides cleansing action by removing pollutants, organic detritus and bottom sediments, which drain into the bay from the lands above (Storm, 1972; University of California Cooperative Extension, 1995; National Park Service, 2001). 3.1.2 Circulation, sedimentation, nutrient levels and water borne pathogens Hydrographic studies of Tomales Bay have documented the bay’s metabolism, its water composition, the dynamics of its nutrient circulation, and the influence of coastal upwelling, among other topics. Among the first such study was Johnson, et al.’s 1961 Ecological survey of Tomales Bay: preliminary report of the 1960 hydrographic survey. Additionally, Tomales Bay has been the subject of an intensive study into the biogeochemistry of estuaries (e.g. Smith et al. 1987, 1989, 1991, 1996; Hollibaugh et al. 1988, 1991). Cole et al. studied the hydrographic, biological and nutrient properties of Tomales Bay (1990). Chambers et al. (1995) studied the nitrogen and phosphorus dynamics in fringing tidal marshes of the bay. Circulation and nutrient dynamics in Tomales Bay are predominantly influenced by the bay’s physical shape, tidal cycles and watershed run-off. The linear shape of Tomales Bay and its narrow mouth place constraints on tidal exchange with the ocean. As a result, salinities in the southern end of the bay are highly variable, ranging from nearly fresh after heavy winter runoff to slightly hypersaline in summer, whereas regular tidal mixing at the north end of the bay maintains salinities that consistently reflect those of the outer coastal waters (Hollibaugh et al., 1988; Kelly and Tappen, 1998). The average annual maximum tidal swing is 2.5 m, with a difference between mean high and mean low tide of about 1.1 m. Water in the northern six km of the bay exchanges with nearshore coastal water on each tidal cycle, while water in the southern 14 km of the bay is resident for approximately 120 days Tomales Bay Watershed Stewardship Plan: A Framework for Action 25

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during times of low runoff (Hollibaugh et al., 1988). In winter, water residence time is determined by the amount of freshwater inflow. Tomales Bay exhibits significant variations in nutrient and salinity levels throughout the year, due largely to the varying strength of offshore coastal upwelling and changes in the freshwater inflows (Niemi and Hall, 1996). Tomales Bay has two seasons of nutrient inputs: rainfall and surface water runoff are high in the winter months (November - April); in the summer (May - October), stream flow and runoff to the Bay are greatly reduced. Nutrient cycling in the bay is driven by the decomposition of organic material, which includes microscopic phytoplankton, macroscopic algae seaweeds, and terrestrial plants deposited from the land above the bay and nutrients from coastal upwelling. Most of the organic material is consumed within the bay, and supplies energy for secondary production (Smith et al., 1996). The influence of nutrient rich run-off into the bay and tributary streams from agricultural lands and septic systems throughout the watershed is greater in the inner bay, which extends from Pelican Point to the Lagunitas Creek estuary. In this area tidal dispersion has less of an effect than density-driven circulation. Coastal upwelling of the California current, which is the primary oceanographic influence in Tomales Bay, provides cool seawater with elevated nutrient levels and high primary productivity. The influence of coastal upwelling is greatest in the outer bay, defined as the area from Pelican Point to Sand Point. This area receives the greatest flushing from tidal exchange, which transports nutrients that are brought up by coastal upwelling. This upwelling is episodic, dependent upon the northerly winds, and tends to be strongest between April and September (Bakun, 1975). This period coincides with that of the minimum freshwater flow in the dry summer. Sedimentation is rapidly occurring in Tomales Bay. Comparisons were made between 1861 and 1957 using hydrographic charts with corrections made for changing sea levels (Rooney, 1999). These calculations showed a bay wide average infilling rate of 5mm/yr. This is equivalent to a watershed erosion rate of approximately 80,000 tons per year. The largest sediment influx seems to have occurred between about 1930 and 1960. The physical filling of the bay reduces the water volume, alters circulation patterns, changes nutrient levels, effects benthic communities and estuary habitat in general, and it also can effect the contaminant load in the bay. Mercury attached to fine particles has moved--and most likely will continue to move--into Tomales Bay. Phosphate and coliform bacteria can attach to particles and be transported and deposited into the bay as sediment. Re-suspension can occur during high winds and winter runoff, thus exposing the system to new pulses of contaminates. Please see appendices for a more detailed discussion on water quality status and trends, and on sedimentation in the bay and watershed. Nutrient levels in the bay are closely linked to sediment movement since many nutrients can attach to fine particles and deposit as sediment. Because balanced nutrient levels are critical in maintaining the bay ecosystem, it is important to distinguish natural levels from elevated concentrations coming from animal and human activities in the watershed. This is not a simple task since nutrient levels often involve complex relationships between sediment and the water column, storage in ponds and sediment sinks and seasonal variability. Tomales Bay Watershed Stewardship Plan: A Framework for Action 26

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Bacteria are a common indicator of water borne pathogens that can be injurious to humans and other living organisms, and may indicate the presence of viruses and parasites, in addition to other types of water contamination that are more difficult to assess. Mariculture requires relatively high water quality. Thus agencies with responsibility for water quality have in the last 20 years done extensive work to investigate the cause, frequency, and sources of bacterial contamination of shellfish in Tomales Bay. These bacteria-focused studies have dealt primarily with total and fecal coliform from a number of possible sources, including dairies and ranches, from substandard or failing sewage systems, and from natural populations of wildlife that live in or visit the bay and surrounding watershed. All of the bacterial studies reviewed in the development of this Plan have indicated that animal-based agricultural runoff plays a major role in the high levels of fecal coliform recorded in Tomales Bay and its tributaries during the rainy season (see appendices for additional information). In order to address this problem, local dairies in the watershed joined together to create the TBAG in 1999 to collectively address common management issues. To assist TBAG with their water quality efforts, the University of California Tomales Bay Water Quality Project has implemented a “systems approach” to study animal agricultural facilities in order to identify possible links between animal agriculture and fecal coliform-, nutrient-, and sediment-loading to the bay. In addition, the San Francisco Bay RWQCB, the California Department of Health Services (DHS), Marin County Environmental Health Services (EHS), and other agencies have on-going water quality monitoring programs to track pathogen levels and other water quality parameters in Tomales Bay and tributary streams. 3.2 Catchment area and tributaries The Tomales Bay watershed comprises an area of approximately 220 square miles and has two main tributaries, Walker and Lagunitas creeks (State of California Department of Health Services, 2002). The catchment area for Tomales Bay is a rural watershed of mostly parklands and pastureland with low human population density. Topography in the 76-square mile Walker Creek sub-watershed ranges from 1,500 feet to sea level, where the creek empties into Tomales Bay just south of its mouth. The northern tributaries, Keyes Creek and Chileno Creek, flow through wide valleys with gentle, grassy hills. The upper watershed is much more rugged with extensive areas of coast live oak forest. Soils, underlain by Franciscan formation sandstone and shale, are highly erodible (Kashiwagi, 1985). This sub-watershed contains a 220-acre natural lake, Laguna Lake, at the top of Chileno Valley. Soulajule Reservoir, constructed in 1968 in Arroyo Sausal and enlarged in 1980, is managed by the MMWD. Since European settlement, land use in the Walker Creek watershed has been almost exclusively agricultural. The only concentrated development in the watershed occurs in the small town of Tomales. At 103-square miles, the Lagunitas Creek watershed is the largest drainage to Tomales Bay. It differs greatly from Walker Creek in many ways. First, rainfall in the upper watershed averages 50 inches per year, compared to 25 in Chileno Valley. Halleck Creek, Nicasio Creek, San Geronimo Creek, and mainstem Lagunitas through Samuel P. Taylor State Park Tomales Bay Watershed Stewardship Plan: A Framework for Action 27

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have areas of dense redwood growth and cool water year round. Except for a few open areas, most of Lagunitas Creek downstream of the state park is thickly forested with willows and alders. Lagunitas Creek is fed by six main tributaries: Olema, Nicasio, San Geronimo, Bear Valley, Devil’s Gulch and Deadman’s Gulch creeks (Niemi and Hall, 1996). Much of the streamflow in mainstem Lagunitas Creek is regulated by dams and collected into various reservoirs upstream of the San Geronimo confluence, with Olema and San Geronimo creeks being the largest uncontrolled tributaries. Olema Creek is the largest tributary in the Lagunitas Creek watershed, flowing for nine miles along the San Andreas Fault Zone, with a catchment area of 14.5 square miles (PRNS, 2001). Olema Creek and tributaries provide significant fisheries and aquatic habitat. Over half of the watershed is in public ownership with a corresponding increase in opportunities for consistent, comprehensive management. Ranching, on both private lands and on land leased from the NPS, continues in the Olema and Nicasio Valleys, and in lower Lagunitas. The Lagunitas Creek watershed also contains many small communities, namely: Woodacre, San Geronimo, Forest Knolls, and Lagunitas in San Geronimo Valley, Nicasio, Olema, and Point Reyes Station. The upper part of the watershed is owned and managed by MMWD for water supply to east Marin County. MMWD has five reservoirs in the watershed - four on mainstem Lagunitas Creek, and Nicasio Reservoir on Nicasio Creek. There are a number of small streams on the east and west shores that flow directly into Tomales Bay. These small streams drain approximately 30 square miles of the Tomales Bay watershed. On the eastern shores, these streams include Tomasini Canyon and Millerton Creek among various others. Western shore streams include Haggerty Gulch, Trout Hatchery Creek, Redwood Creek, and First, Second and Third Valley creeks. 3.3 Climate Wet, rainy winters and dry summers characterize the Mediterranean climate of the region. Depending on location within the watershed, the 120-year average rainfall ranges from approximately 30 to 61 inches per year with 95 percent of the precipitation occurring from October to April (Fischer et al., 1996). Variations in climate are most affected by proximity to the coast. During most of the year the ocean water temperatures near the coast are lower than that of the ocean to the west. The cooling effect of these cold coastal waters on the warmer moist air moving inland produces fog. The result is blankets of fog for more than 50 miles off shore and into inland areas that include the majority of the watershed (Evens, 1993). These heavy fogs are most common in July, August and September, and provide an important source of precipitation along the coastal areas of the Tomales Bay watershed. Further inland, there is more sunshine and temperatures are higher. 3.4 Geology Geologic studies of the Tomales Bay watershed began as early as the late 1800’s and have continued until present time. In addition to the references summarized below, contributing Tomales Bay Watershed Stewardship Plan: A Framework for Action 28

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authors include Johnson et al., 1961; Daetwyler, 1966; Smith et al., 1971; Wahrhaftig and Wagner, 1972; Galloway, 1977; Blake, 1856; Anderson, 1899; Johnson et al., 1961; Northern California Geological Society, 1989. Daetwyler (1966) provided an account of the marine geology of Tomales Bay. The Tomales Bay watershed consists of three general physiographic regions: the rugged California Coast Range along the western edge of the watershed; nearly level alluvial fans, alluvial plains, and floodplains in intermountain valleys; and low-lying tidal marshes (U.S. Department of Agriculture et al., 1985). Tomales Bay is a submerged valley along the San Andreas Fault. The bay was formed 15,000 to 5,000 years ago when it was inundated by rising sea levels from thawed ice at the close of the last ice age (Wahraftig and Wagner, 1972). The San Andreas Fault serves as a divide between two distinct underlying geologic easements, the Pacific and the North American Plates. This fault is the most significant geological feature in the watershed, influencing the geology, topography and overall stability of the area. Tectonic pressure causes these two plates to move in opposite directions resulting in periodic seismic activity. Evidence suggests that in the past 25 million years the Point Reyes Peninsula has been moving northward at a rate of 0.5 inches per year (Galloway, 1977). San Francisco's 1906 earthquake, however, caused the Peninsula to shift12-13 inches to the north in a matter of seconds (Evens, 1993; Shuford and Timossi, 1989). The northeast portion of the Tomales Bay watershed is comprised of the Franciscan Formation and includes Mesozoic marine sandstones, shales, chert, serpentine, and volcanic rocks that were deposited as lava flows about 80-140 million years ago (Wahrhaftig and Wagner, 1972; Shuford and Timossi, 1989; University of California Cooperative Extension, 1995). This Formation is susceptible to landslides and debris flows and is more likely to erode and gully than other areas of the watershed excluding the Wilson Hill Formation (University of California Cooperative Extension, 1995). North of Walker Creek, another sedimentary complex, the Wilson Hill Formation, was deposited over the Franciscan Formation about 5 million years ago. This formation consists of sand, silt, and clay that has uplifted and eroded, leaving remnants on the hilltops. Wahrhaftig and Wagner (1972) suggest the Wilson Hill Formation is less likely to develop landslides than much of the Franciscan complex, but it is also highly erodible and easily gullied. Earthquakes have played and still do play a role in the geologic activity along the active San Andreas Fault. The effects of the 1906 earthquake resulted in crater-like depressions in Tomales Bay that developed along the surface fault trace on Sand Point and gently undulating ridges and troughs covering the tidal mud flats at the southern end of the bay. Horizontal shifting of mud was also observed near the bayshore in the vicinity of Inverness (Smith et al., 1971). 3.5 Soils The Soil Survey of Marin County California describes the soils in the Tomales Bay watershed and the rest of Marin County in relationship to the geology, landforms, relief, climate and natural vegetation (U.S. Department of Agriculture et al., 1985). This survey Tomales Bay Watershed Stewardship Plan: A Framework for Action 29

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includes a description of soils and miscellaneous areas and their location; in addition to a discussion of their suitability, limitations, and management for specified uses. Several major soil type associations are found throughout the Tomales Bay watershed. In general, the soils on the western shore are coarse-grained, well drained soils of granitic origins and those on the eastern shore are finer soils from tectonic mélange origins derived from the Franciscan and Wilson Hill formations. Soil types reflect the diverse underlying geology of the watershed and influence the plant communities that they support (Evens, 1993). 3.6 Fire History Mediterranean climates create ideal fire-prone conditions for the spread of natural and human set fires (Pavlik et al., 1991). Large fires are known to have occurred in the watershed in 1887, 1927, 1945, and most recently, in 1995 (Evens, 1993; Howell, 1970; National Park Service, 1996). According to recent research completed by the PRNS, there is evidence from dendrochronological (tree) records and from sediment core analyses that periodic fire has occurred in the Point Reyes Peninsula for the past several thousand years, and ecosystems in the area have developed under the influence of these fires. Several native plant species in the area (e.g. Bishop pine, Marin manzanita) reproduce most abundantly following fire. For the past 100 years, however, fire frequency has decreased, and most fires have been suppressed. It is clear that a lack of periodic fire during this period has resulted in changes in vegetation structure and species composition. Although there are no quantitative data on the magnitude of these changes, it is generally assumed that forest stand density in many areas has increased, shrub and grassland habitats in many areas are being reduced in size due to encroachment by conifers. This pattern is not universal throughout the Tomales Bay watershed and the grasslands and hardwood forests of the eastern portion of the watershed may have historically burned at different intervals. 3.7 Biological Resources The Tomales Bay watershed and adjacent coastal marine waters are biologically significant because the mild climate of the watershed allows for a mosaic of aquatic and terrestrial habitats. The diverse spectrum of habitats and flora result from factors, which include its evolutionary and geological history, varied topography and soils, and fire and disturbance regime. These habitats predominantly include Douglas fir, bishop pine and mixed evergreen forests; oak woodlands; annual and perennial grasslands; freshwater and saline wetlands; coastal dunes and prairies; tidal flats composed of mud and sand; eelgrass beds and open waters of the bay. These habitats sustain a rich diversity and abundance of plant and animal life, as they provide critical shelter, foraging, nesting and rearing habitat. Nearly 900 species of plants, hundreds of species of birds, hundreds of invertebrate species, and numerous sensitive, threatened and endangered species inhabit the watershed and nearby Point Reyes peninsula. Sensitive species include federally listed species such as coho salmon, steelhead trout, brown pelican, Steller sea lion and red-legged frog. Other sensitive species that have state or local Tomales Bay Watershed Stewardship Plan: A Framework for Action 30

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significance include tule elk, Point Reyes jumping mouse, and river otter. These ecosystems also serve as refuges for populations of rare plants. The Tomales Bay watershed functions both as a place of residence for numerous species and also a significant transition zone for those animals that visit seasonally or migrate through. The amount of biomass associated with the watershed, therefore, varies by season and year. For example, the open waters, tidal flats, and marshes of Tomales Bay provide critical resting and foraging grounds for a great diversity and abundance of animals that include: several hundred seals and sea lions, and 20,000 wintering shorebirds and up to 25,000 waterbirds use the bay each year along their migration route on the Pacific Flyway that have been sighted here during annual surveys (Allen et al., 2002; Kelly, 2001). The bay also provides important foraging, spawning and nursery habitat for many marine and anadromous fish species, such as young of the year boccacio rockfish, which utilize the natural abundance of food and shelter in Tomales Bay’s eelgrass beds; and Pacific herring which use the bay for their annual spawn and in turn provide an important food source for marine mammals, bird and fish species. Habitat loss, species decline and exotic species are a significant concern in the Tomales Bay watershed. For example in Tomales Bay, the introduction and spread of European green crabs (Carcinus maenas) has led to major declines of several key invertebrate species as a result of predation by these crabs, which may in turn affect shorebird populations that feed on these invertebrates (Grosholz, 2000). On Tom’s Point and nearby lands adjacent to Tomales Bay, coastal terraces have been overrun by invasive non-native perennial grasses (D’Antonio et al., 2003). Additionally, the current status of coastal prairie around Tomales Bay is strongly influenced by the expansion of invasive non-native perennial grasses such as velvet grass (Holcus lanatus) and tall fescue (Festuca arundinaceae) (D’Antonio et al., 2003). Between the bay and coastal terraces, the potential for invasion by smooth cordgrass (Spartina alterniflora) is a constant threat to Tomales Bay due to nearby colonies and the capacity of this species to hybridize with native Spartina populations (Ayres, 2000). Smooth cordgrass, a native to the eastern U.S., converts tidal flats to meadows, with resulting profound impacts on shore and nearshore habitats in bays and estuaries along the western coast, and monitoring is on-going. Management of these and other invasive non-native species is a complex and uncertain proposition, and protection and enhancement of local populations of native organisms and restoration of degraded habitats will be a significant challenge in the future.

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Literature Cited Allen, S.G., H.R. Huber, C.A. Ribic, and D. G. Ainley. 1989. Population dynamics of harbor seals in the Gulf of the Farallones, California. Calif. Fish and Game, 75:224-232. Allen, S., S. Waber, D. Press. 2002. Long-term monitoring of harbor seals at Point Reyes, California. Five year annual report, 1997-2001. National Park Service publication. Anderson, CF. M. 1899. The geology of Point Reyes peninsula: University of California Publications, Bulletin Department of Geology, v. 2, no. 5, p. 119-153. Ayers, D. 2000. Spartina in Tomales Bay – Friend or Foe? Proceedings of the Fourth Conference on the State of Tomales Bay. Bakun, A. 1975. Daily and weekly coastal upwelling indices, west coast of North America, 1946-1971. National Oceanic and Atmospheric Administration Technical Report NMFS SSRF-693. Bellinger, T. 1995. Point Reyes National Seashore Water Resources Management Plan. National Park Service Water Resources Division and Point Reyes National Seashore, Technical Report NPS/NRWRD/NRTR-95. Second Draft 70 pp. Blake, W. P. 1856. Geology of Punta de Los Reyes Peninsula. In: report to the Superintendent of the U.S. Coast Survey for 1855. Geological Report No. 65. California Regional Water Quality Control Board. 2001. Controlling Pathogens in Tomales Bay, California: Total Maximum Daily Load: Sources and Loadings, Progress Report. CRWQCB, San Francisco Bay Region. 31 pgs. + tables and figures. California State Coastal Conservancy. 1984. A Program for Restoring the Environment of Tomales Bay. State Coastal Conservancy, Oakland, California. 28 pgs. Chambers, R.M., J.W. Fourqurean, J.T. Hollibaugh, and S.M. Vink. 1995. Importance of terrestrially-derived particulate phosphorus to P dynamics in a west coast estuary. Estuaries, 18(3):518-526. Cole, B. E., S. W. Hager and J. T. Hollibaugh. 1990. Hydrographic, biological and nutrient properties of Tomales Bay, California, March 1985 to May 1986. U.S. Geological Survey Open File Report 90-178. Corwin, Ruthann (prepared by). 1972. Tomales Bay Environmental Study Compendium of Reports. Marin County, California. County of Marin. 1981. Marin County Local Coastal Program, Unit II. Daetwyler, C.C. 1966. Marine Geology of Tomales Bay, Central California. Scripps Institution of Oceanography: research Report No. 6. 169 pp. D’ Antonio, C. M. and J.D. Corbin, pers. comm. 2003. University of California, Berkeley, Integrative Biology Department. Evens, J. G. 1993. The Natural History of the Point Reyes Peninsula. Revised Edition. Point Reyes National Seashore Association. 224 pp. Fischer, D. T., S. V. Smith, and R. R. Churchill. 1996. Simulation of a century of runoff across the Tomales watershed, Marin County, California. Journal of Hydrology 186: 253-273. Galloway, A. J. 1977. Geology of the Point Reyes Peninsula, Marin County, California. California Division of Mines and Geology Bulletin 202. Sacramento, CA. Grosholz, Edwin. 2000. Impacts of Introduced Species on Coastal Food Webs and Aquaculture in Tomales Bay, pg. 10. Proceedings of the Fourth Conference on the State of Tomales Bay. Tomales Bay Watershed Stewardship Plan: A Framework for Action 32

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Hollibaugh, J. T., B. E. Cole, S. J. Dollar, S. W. Hager, S. M. Vink, W. J. Kimmerer, S. Obrebski, S. V. Smith, M. Valentino and T.W. Walsh. 1988. Tomales Bay, California: A macrocosm for examining biogeochemical coupling at the land-sea interface. Eos 69:843-845. Hollibaugh, J. T., R. W. Buddemeier, and S. V. Smith. 1991. Contributions of colloidal and high molecular weight dissolved material to alkalinity and nutrient concentrations in shallow marine and estuarine systems. Marine Chemistry 33: 1-27. Howell, J. T. 1970. Marin Flora. Univ. of Calif. Press, Berkeley, CA. Johnson, R.G., W.R. Bryant, and J.W. Hedgpeth. 1961. Ecological survey of Tomales Bay: preliminary report of the 1960 hydrographic survey. [Bodega Bay, Calif.] : Pacific Marine Station, University of the Pacific, Series title: Research reports; no. 1. 19. Kashiwagi, J.H. 1985. Soil Survey of Marin County. U.S. Department of Agriculture, Soil Conservation Service. Kelly, J.P. 1992. Bird populations on Tomales Bay. Pages 28-32 in Wyatt, B., R. Clutter, and L. Sauter, eds. The Third Biennial State of Tomales Bay Conference. Inverness Foundation, Inverness, California. Kelly, J.P. 2001. Distribution and abundance of winter water birds on Tomales Bay, California: implications for conservation. Western Birds 32:145-166. Kelly, J.P. and S. L. Tappen. 1998. Distribution, abundance, and implications of conservation of winter waterbirds on Tomales Bay, California. Western Birds 29:103-120. Marin County Resource Conservation District (MCRCD). 1965. Master Drainage and Sediment Control Plan. Lagunitas & Walker Creek Watersheds. June 1965. National Park Service (NPS), U.S. Department of the Interior (U.S. DOI). 1995. Tomales Bay/Bodega Bay Watershed Boundary Study. Point Reyes National Seashore. NPS, U.S.DOI. 1996. Vision Fire: Rehabilitation Begins. Point Reyes National Seashore. NPS, U.S. DOI. 2001. Tomales Bay: Guidelines for Protection and Use. Point Reyes National Seashore, 33 p. Niemi, T.M. and N.T. Hall. 1996. Historical changes in the tidal marsh of Tomales Bay and Olema Creek, Marin County, California. J. Coast. Res. 12: 90-102. Northern California Geologic Society. 1989. Geologic Guidebook to the Point Reyes Area, Northern California. Bruce J. Bilodeau, ed. Pavlik, B. M., P. C. Muick, S. G. Johnson, and M. Popper. 1991. Oaks of California. Cachuma Press and the California Oak Foundation. Oakland, CA. 184 p. PRNS (Point Reyes National Seashore), NPS. 2001. Water Quality Monitoring Report May 1999-May 2001. Prunuske Chatham, Inc. 1997. Lagunitas Creek Sediment and Riparian Management Plan. Prunuske Chatham, Inc., Occidental, California. Prepared for the Marin Municipal Water District. Prunuske Chatham, Inc. 2001. Walker Creek Watershed Enhancement Plan. Prunuske Chatham, Inc., Occidental, California. 55 pgs. Prepared for Marin County Resource Conservation District. Rooney, J. J. and S.V. Smith.1999. “Tomales Bay, California, sedimentation rates and watershed landuse.” Journal of Coastal Research 15(2):478-485. Shuford, W. D. and I. C. Timossi. 1989. Plant communities of Marin County. California Native Plant Society publication. 32 pp. Tomales Bay Watershed Stewardship Plan: A Framework for Action 33

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Smith, E.H., R.G. Johnson, and S. Obrebski. 1971. Physical, chemical, microbiological and hydrographic characteristics of Tomales Bay. University of the Pacific, Stockton, California, Pacific Marine Station Research Report 9: 70 . Smith, S. V., W. J. Wiebe, J. T. Hollibaugh, S. J. Dollar, S. W. Hager, B. E. Cole, G. W. Tribble, and P. A. Wheeler. 1987. Stoichiometry of C, N. P, and Si fluxes in a temperate-climate embayment. Journal of Marine Research 45: 427-460. Smith, S. V., J. T. Hollibaugh, S. J. Dollar, and S. Vink. 1989. Tomales Bay, California: a case for carbon-controlled nitrogen cycling. Limnology and Oceanography 34: 37-52. Smith, S. V., J. T. Hollibaugh, S. J. Dollar, and S. Vink. 1991. Tomales Bay metabolism: CN-P stoichiometry and ecosystem heterotrophy at the land-sea interface. Estuarine, Coastal and Shelf Science 33: 223-257. Smith, S. V., R. M. Chambers, and J. T. Hollibaugh. 1996. Dissolved and particulate nutrient transport through a coastal watershed-estuary system. Journal of Hydrology 176: 181203. Smith, S. V., and J. T. Hollibaugh. 1997. Annual cycle and interannual variability of ecosystem metabolism in a temperate climate embayment. Ecological Monographs 67: 509-533. State of California Department of Health Services. 2002. Twelve-Year Sanitary Survey Report: Shellfish Growing Area Classification for Tomales Bay, California. Technical report no. 02-04. Division of Drinking Water and Environmental Management, Environmental Management Branch, Environmental Health Services Section, Preharvest Shellfish Sanitation Unit. Storm, D. R. 1972. Hydrology and water quality aspects of the Tomales Bay Study, in Tomales Bay Environmental Study (R. Corwin, ed.), pp. 84-101. Conservation Foundation, Washington, D.C. Suer, A. L. 1987. The Herring of San Francisco and Tomales Bays. The Ocean Research Institute, San Francisco, CA. 64 pp. Tomales Bay Watershed Council. 2002. Bulletin Winter 2002. University of California Cooperative Extension (UCCE). 1995. The Marin Coastal Watershed Enhancement Project. University of California Cooperative Extension. Novato, California. 83 pgs. U.S. Department of Agriculture, Soil Conservation Service, U.S. Department of the Interior, National Park Service, and the U.C. Agricultural Experiment Station. 1985. Soil Survey of Marin County, California. Wahrhaftig, C. and J.R. Wagner. 1972. The geologic setting of Tomales Bay. Tomales Bay Environmental Study. In Tomales Bay Environmental Study, (Ed.) Corwin, Ruthann. The Conservation Foundation, Washington D.C.

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B. HUMAN USES OF NATURAL RESOURCES “Tomales Bay and the agricultural landscape that function as its watershed are defining elements of Marin County’s extraordinary environmental quality and basic character, and both are threatened. To save them will require the cooperation and concerted effort of everyone who cares about habitat conservation, family farming, and open space preservation.” -- Bob Berner, Marin Agricultural Land Trust 2002

1.0 Introduction For thousands of years an indigenous people that have come to be recognized as the Coast Miwok occupied the Tomales Bay watershed. The natural abundance and mild climate of the watershed seems to have provided more than ample existence for these people. Historic accounts and archeological data suggest that a large resident population lived peaceful simple lives, hunting and gathering most of what they needed and trading with neighboring tribes for the few essentials that were not readily available (Treganza, unknown). The early 1800’s saw the end of the Coast Miwok way of life. The occupation of the territory by Mexico and the subsequent land grants, the construction and operation of Mission San Rafael and its shepherding/enslavement of many of Marin’s indigenous people, and of most consequence, the introduction of the smallpox virus effectively displaced and extinguished this tribe. Survivors were marginally assimilated into the ever-expanding cultural landscape. Recently, Congress granted limited legal tribal status to the Council of the Federated Coast Miwok of the Graton Rancheria. The Mexican, Spanish and subsequent European settlement of the area brought with it changing land use practices, and different natural resource based economies. Today, the primary land uses in the Tomales Bay watershed are livestock grazing, dairy farming, lowdensity residential, municipal water supply and parklands. Two thirds of the land in the watershed is zoned agricultural, primarily used for cattle, with some sheep ranching and organic farming. The watershed also supports significant recreational activities that include hiking, birding, boating, camping, bicycling, picnicking, clamming, fishing, and the collecting of wild mushrooms and berries. The abundant recreational attractions in the watershed and surrounding area create a substantial market for visitor-serving enterprises. Much of the local economy is predicated upon the demand for recreation-oriented goods and services ranging from over-night accommodations to kayak rentals to numerous restaurants and eateries. Tomales Bay also supports the commercial cultivation and harvesting of shellfish, including oysters, mussels, and clams, as well as commercial and recreational fishing. Of the 140,094 acres in the watershed, approximately 70 percent is privately owned; and the rest is either publicly owned or lands of the Marin Municipal Water District (Press, 2001). Tomales Bay Watershed Stewardship Plan: A Framework for Action 35

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Undeveloped public lands occupy the majority of the northwestern watershed, and this land is habitat for a diversity of wildlife, some of which is also used for livestock grazing and other agricultural practices. Eleven towns comprise approximately 10 percent of the watershed and include both commercial and residential use. On the shores of the bay there are a number private homes in addition to commercial operations that include hotels and bed and breakfasts, a resort, oyster farms, kayaking businesses, boat works, and restaurants (UCCE, 1995).

2.0 Residential Development, Water Supply and Waste Management There are eleven small towns within the Tomales Bay watershed with a combined residential population of approximately 11,000. Most of these towns originated as fishing and agricultural villages and summer vacation destinations. Today, residential communities in the watershed include: Inverness, Inverness Park and Marshall along the periphery of the bay; Olema, along Olema Creek; Woodacre, San Geronimo, Forest Knolls, and Lagunitas along San Geronimo Creek; Nicasio on Nicasio Creek; and Point Reyes Station near the mouth of Lagunitas Creek. In the northern part of the watershed are the towns of Tomales and Dillon Beach, which includes Lawson’s Landing- a commercial facility with approximately 233 full-time trailers and 1,000 additional camping sites and hook-ups (County of Marin, 1981; UCCE, 1995; Shannon and Associates, 1997). Groundwater, springs and surface water provide domestic water supply in the Tomales Bay watershed. The volume of these systems correlates with annual precipitation, and must be recharged each year during the rainy season. The larger subwatersheds (e.g. San Geronimo Creek, Nicasio Creek, etc.) have storage reservoirs, the largest being owned by Marin Municipal Water District. Agricultural properties also have impoundments on smaller tributaries in the Tomales Bay watershed, but these are usually used for stock rather than domestic supply. The MMWD supplies water to residential and agricultural water users in both West and East Marin; a total of 185,000 people in Marin County. 75 percent of the water MMWD supplies originates in the Lagunitas Creek watershed, where streamflow is collected into a series of large-scale reservoirs (for additional information on freshwater inflow and hydrology see Section II, part 3.5.1). The Russian River (which is significantly augmented by water from the Eel River) supplies the remaining 25 percent of the water supply MMWD provides to Marin County. Nicasio and Soulajule Reservoirs provide 40 percent of MMWD’s storage capacity and 15 percent of their annual consumption. There are two MMWD water treatment plants, one within the San Geronimo Valley and another near the Bon Tempe Reservoir. In addition to MMWD, domestic water supply is provided by residential wells, the North Marin Water District (NMWD) and the Inverness Public Utility District. There are wells in remote or higher elevation areas along the Inverness Ridge, and on some of the agricultural properties in the Walker Creek watershed. The villages around the south end of Tomales Bay- Olema, Pt. Reyes Station and Inverness Park- rely on NMWD for their water supply systems. Wells adjacent to Lagunitas Creek near Point Reyes Station and tank storage Tomales Bay Watershed Stewardship Plan: A Framework for Action 36

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provide water for these villages. The Inverness Public Utility District supplies the town of Inverness with its own water system, relying on springs, catchment basins and tank storage. Small wells, springs and a couple of cisterns serve Marshall, on the east shore of the bay. The Marin County EHS estimates that there are approximately 7,000 septic systems in Marin County. The typical pattern in the county is a single family dwelling with its associated septic system for which the property owner is responsible. These systems vary from redwood box cesspools to highly engineered modern pressure dosed systems. There is information for approximately half of the septic systems in the watershed, particularly for systems that have been permitted since 1984 when new septic regulations were adopted. However, there is not a complete inventory for all septic systems at this time and an accurate figure for the number of septic systems in the Tomales Bay watershed is unavailable. Based on the current records, there are 212 septic parcels within 100 feet of the bay or a creek on the west shore, and 186 on the east shore. There are 808 septic parcels within 100 feet of a creek or reservoir in the Lagunitas Creek watershed including Olema Valley, and 100 within the Walker Creek watershed (Tuden, 2002). There is substantial variation within these parcels, some are fractional acreage and others are several hundreds of acres. Many of the septic systems on these parcels are immediately adjacent to water bodies while others are hundreds of yards away. Currently, EHS is developing a program that will provide a comprehensive inventory that will include location, type of system, and an evaluation of system function and associated environmental risk. In addition, EHS is in the process of reviewing septic permitting procedures and some sort of operation and maintenance process is anticipated in the next few years. There are both documented water quality exceedences and additional threats to water quality from deficient septic systems in the Tomales Bay watershed. There are nine permitted sewage treatment systems in the Tomales Bay watershed that are regulated by the San Francisco Bay RWQCB, namely: the Tomales Wastewater Treatment Plant, Marconi Conference Center, Borello Sewage Ponds, Skywalker Ranch, Olema Ranch Campgrounds, Samuel P. Taylor State Park, Blue Mountain, Spirit Rock and Walker Creek Ranch. These systems vary in their treatment methods, waste sources and capacities. The San Francisco Bay RWQCB regulates all of these facilities through their waste discharge permitting system because of the size of the facility or the treatment methods used. Some of these facilities produce sewage onsite (e.g. Samuel P. Taylor State Park), while others receive waste from haulers (e.g. Borello Sewage Ponds). Treatment methods at these facilities range from digesters with primary and secondary treatment, to holding ponds and subsequent spreading of liquids and solids. The low population density and policies in West Marin have sustained the use of septic systems in the Tomales Bay watershed. West Marin has been a long-time target for urban development, primarily due to its proximity to the San Francisco Bay Area. In 1964, the West Marin Preliminary Master Plan envisioned a population of 66,330 in West Marin, although the population in the area at the time of the report was 2,271, and the plan slated the area for the development of large estates, cluster housing and commercial centers. If this had

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come to pass, residential septic systems would not have been adequate to handle the waste generated by such development. During four years of re-zoning in this area (from 1972 to 1975) the number of potential building sites in the watershed was reduced from 1.2 million to 3,000. Two thirds of the land in the Tomales Bay watershed today is A-60 zoned, with a 60-acre minimum parcel size for agricultural lands in the Master Plan for Marin County (County of Marin, 1981). These actions and the creation of the PRNS, GGNRA, and various other State and County parks in the watershed have preserved open space in this watershed and the western two-thirds of Marin County. While the established parklands will protect the open space in the watershed in perpetuity, the local zoning of this area can change by a vote of the County Board of Supervisors.

3.0 A Historical Overview of Land Use in the Watershed 3.1 History of agriculture in the watershed “Land stewardship plays an important role in protecting the health of Tomales Bay and the viability of agriculture. In return, as a rancher my quality of life and the quality of my operation depend upon clean water, good forage, and productive soils created by a healthy watershed.” -- Bob Giacomini, Tomales Bay Agricultural Group Because of the productivity of the lands of the watershed, Tomales Bay watershed has provided agricultural commodities to the Bay Area and local communities for much of the last two centuries. Mexican land grants in the 1830s led to the establishment of the first rancherias in the area. The European farmers and ranchers that replaced the Mexican landholders were from diverse backgrounds including Irish, Italian, Swiss, and Portuguese. Production of animal and crop agricultural goods increased in response to demands for food and fiber associated with the 1849 Gold Rush in California. Through this production history, the importance of different agricultural commodities produced in the watershed has ebbed and flowed. Influences have included the suitability of land and climate for producing various commodities, response to market forces, increasing environmental stewardship, and policies that support and regulate agriculture. Long ago farmers recognized the soil and climate in the watershed, specifically around the town of Tomales, as favorable for growth of potatoes. Sea fogs during the summer promoted potato growth, while grains such as wheat and barley did better inland around Chileno Valley. In 1860, 33 of 75 farms in the area were producing potatoes and 26 of these produced more than 1,000 bushels. By 1862 Marin was fourth in the state for potato production (133,500 bushels), most of which was occurring in the northern part of the county. By 1880 almost every farm and ranch was tilling at least 25 acres of land for potatoes and other crops including wheat, oats, and barley. Potato production averaged 600 to 2,000 bushels per farm. By the 1930s potato production had declined or virtually stopped Tomales Bay Watershed Stewardship Plan: A Framework for Action 38

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as varieties compatible with watershed soils and climates lost their popularity and production elsewhere in the state out-competed production in Marin County. The same climate and soil conditions that were favorable for potato production were also recognized as contributing to productive rangelands for animal agriculture within the watershed. Some of the earliest animal agriculture production in Marin County (which included production on the Point Reyes Peninsula, and other areas beyond the Tomales Bay watershed) and the watershed was beef cattle for hides and tallow. Sheep became an important commodity in the late 1850s but numbers have been highly variable between years and decades since then. In 1850, Marin County was among the ten leading cattle production counties in the state, with 6,891 head. In 1866, Marin County produced three-fourths of California’s butter- a total of 932,427 pounds (Zumwalt, 1972). Marin County was among the top ten one more time in 1880, with a cattle census of 32,449, most of which were dairy cattle. During the same year, the Sacramento Record-Union reported that Marin and Sonoma County pastures “afford constant, fresh and luxuriant grasses from January to September and October.” After this point in time, cattle production in the Central Valley was well established and out produced the coastal areas (Burcham, 1957). Continuous market influences, cultural changes, regulatory requirements, and state and local policies have shaped the face of agriculture in the watershed today. In 1973, the County of Marin approved its General Plan which divided the county into three sections: coastal and recreational, rural and agricultural including coastal agriculture, and eastern urban. A-60 zoning for agricultural lands in Marin County has protected open space and agricultural land uses in the watershed by controlling the proliferation of development. Within the agricultural zone, one house per 60 acres was allowed where previously one house per two acres was permitted. In addition to this policy, the MALT was founded in 1980 to preserve farmland in Marin County, and has since protected over 32,000 acres through agricultural conservation easements on 46 family ranches and farms. MALT is the first land trust in the nation focused on farmland preservation, and has continued to work with landowners by providing easements via the purchase of development rights on agricultural lands. Currently, there are 10 producing dairies in the watershed located on private and public lands. The rest of the rangeland is used for beef, sheep, and replacement heifers. Many families that are ranching and farming today in the watershed are fourth and fifth generation descendants of the original European farmers and ranchers, and have been working to improve their practices for the last three decades with the assistance of the NRCS, Marin RCD and the UCCE. Some of these families are diversifying their operations and producing for niche markets that include: direct marketing of products, local processing of milk, and production of specialty products like cheeses, grass-finished beef, olives, grapes, strawberries, and vegetables. Today many dairy producers and ranchers are taking steps to address water quality and habitat concerns. In the past these producers have installed waste management systems, with federal, state, and county assistance to collect and store manure according to the guidelines established by the RWQCB’s 1970s “Minimum Guidelines for Protection of Water Quality from Animal Wastes.” TBAG continues to work in collaboration Tomales Bay Watershed Stewardship Plan: A Framework for Action 39

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with the UCCE and other agencies to improve water quality in Tomales Bay and tributary streams by increasing the effectiveness of management practices. In addition, Marin RCD and NRCS continue to provide landowners with both technical and programmatic support for stream restoration, streambank protection, upland erosion control, rangeland management and habitat improvement. Agriculture has clearly played a significant role in both the human and environmental history of the Tomales Bay watershed. Although land use activities have been reduced and modified in many ways, past and present land use continues to influence both habitats and water quality within the watershed. For example, in the interior watershed, grasslands and meadows have been affected by the introduction of non-native grasses via human activities and their spread and colonization has been exacerbated by the plowing of watershed soils for crop production, decades of continuous grazing, in addition to natural cycles of drought. These factors combined have contributed to a shift in the composition of grasslandsultimately reducing the ability of native grasses to compete against introduced European grasses (Bush, 2003; Edwards, 1992; Zumwalt, 1972). Also, in the early decades of the 1900s, several artificial channels were excavated in the Olema Creek watershed. In the early 1920s, Olema Creek was straightened into a 3kilometer long canal between the town of Olema and its confluence with Lagunitas Creek. The canal drained the surrounding land for agricultural production, and feed crops and vegetables were planted. This area has also been used for cattle grazing. Additionally, many of the salt marshes near the mouth of Lagunitas Creek and along the periphery of Tomales Bay were converted into pastureland by the construction of levees during this period (Evens, 1993). As a result, disturbance of the watershed associated with the construction of levees built for railroad or agricultural purposes has increased sedimentation rates and resulted in a reduction of bay water volume and tidal exchange (Niemi and Hall, 1996; Evens, 1993). Additionally, wetland and marsh habitats were lost. Successful enhancement and restoration of terrestrial and aquatic habitats that have been lost or degraded during the last century is critical for the future of the Tomales Bay watershed. Soon the Point Reyes National Seashore will remove levees near the mouth of Lagunitas Creek and undertake a significant restoration program to enhance marsh, floodplain and riparian habitats that were damaged during the last two centuries. Additionally, fisheries and water quality assessments of Olema Creek indicate that the effects of past land use practices have altered the condition of the watershed, affecting its ability to support fisheries at their historic levels, and enhancement and restoration will continue. Residents and agencies are also involved in needed restoration on private lands in many parts of the watershed. See Sedimentation Appendix for a more detailed discussion of the extent, causes, processes and effects of sedimentation on Tomales Bay and the watershed. Changes in native vegetation, soil compaction and loss, hillside trailing, and gullying have altered runoff patterns and reduced the functional capacity of the watershed. On-going programs to protect and support sustainable agriculture, which have included improvements in land use activities and implementation of best management practices, will continue to be important to the changing face of agriculture in the watershed. Tomales Bay Watershed Stewardship Plan: A Framework for Action 40

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3.2 History of mercury mining in the Walker Creek watershed Mercury was a much sought after mineral in California and was used in large quantities during the Gold Rush as an amalgamate, and then later in pesticides, fungicides, pharmaceuticals, paints, and military ignition devices. West Marin was explored extensively for mercury bearing ore from about 1940-1970 and mercury was extracted at seven locations in the watershed: the Cycle and Franciscan Mines which drain to Arroyo Sausal, the Chileno Valley mine which drains to Chileno Creek, and Buena Suerta (the Gambonini mine) which drains to Salmon Creek. A smaller mercury mine also operated on the Robert Dolcini Ranch in the Chileno Creek sub-watershed during the same time as the Gambonini mine, and two more inactive mercury mines are identified in Walker Creek in the Basin Plan (California Regional Water Control Board, 1995). The majority of the mining in the watershed took place between 1968 and 1971 (CDMG, 1972). The largest of these mines, the Gambonini mine, processed its own ore as well as ore from a neighboring mine in the Chileno Creek drainage. It operated as an open pit cinnabar mine for mercury during 1964-1970 on Salmon Creek. By the time the mine closed in 1970, 300,000 cubic meters of mine waste containing 300 tons of mercury had been piled onto 11 acres just upstream of the confluence of mainstem Walker and Salmon Creeks (Whyte and Ganguli, 2000; Kay, 2000). Buttes Gas & Oil, the last operator of the mine, built a tailings dam, contoured the fill, and seeded the site (Thurber, 1970). Following the severe 1981-82 winter the stabilization measures failed. Whyte and Kirchner (2000) estimate that during the stormy winter of 1997-98, the mine site released approximately 1,300 tons of mercury-rich suspended sediments and an undetermined amount of bedload to downstream waters. This suggests that during the even more severe winter of 1981-82, millions of kilograms of sediment entered Walker Creek from the mine. The U.S. Environmental Protection Agency (USEPA), working with the San Francisco Bay RWQCB, completed preliminary remediation of the Gambonini site in 2000. Mercury continues to pose a long-term threat to downstream reaches of Walker Creek and Tomales Bay and further remediation is warranted (Whyte, 2003). 3.3 History of logging, reservoirs and development in the Lagunitas Creek watershed Logging and the production of paper began in the Lagunitas Creek watershed by the 1850s. Logging provided both timber and firewood needed for local enterprises, and the majority of the harvest was shipped to San Francisco. Samuel P. Taylor built the west’s first paper mill on mainstem Lagunitas Creek near Devil's Gulch in 1856. This mill operated 24 hours a day until it closed in 1893. This mill used hydraulic power to process rags and old rope into paper. Logging continued in the Olema Creek Watershed until 1962. In addition to the significant watershed effects associated with large-scale logging, major fires have burned portions of the watershed several times. Additional resource extraction activities included gravel and sand mining from the streambed at the confluence of Lagunitas and Nicasio Creeks until a short time after Nicasio Dam was constructed in 1960. Ranchers regularly harvested small amounts of streambed gravel to maintain ranch roads through the 1980s.

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Lagunitas Creek watershed includes 5 reservoirs that supply water to communities in Marin County- Nicasio Reservoir being the largest with 4 additional reservoirs in the upper reaches of the watershed. Due to the significance of this water supply, much of the Lagunitas Creek watershed is preserved as open space for watershed by the MMWD. Lagunitas Lake, the first of these reservoirs, was constructed in 1872. This reservoir was the first interurban transfer of water in Marin County (Niemi and Hall, 1996). The development of Lagunitas Lake was followed by Alpine Lake in 1919, and then by Bon Tempe in 1949. Peter's Dam, built in 1954 to form Kent Lake, was raised 45 feet in 1982, nearly doubling reservoir capacity from 16,600 acre feet to 33,000 acre feet. These reservoirs have had a significant impact on terrestrial and aquatic habitats. In addition to blocking anadromous fish passage to miles of spawning and rearing habitat, the impoundments have altered streamflows and stopped bedload transport from the upper reaches of the watershed. Road construction has had a significant effect on the Lagunitas Creek watershed. Various roads were built in the late 1800’s, including Bear Valley Road which was built during the time when Olema was the center of commerce in this area (1856-1875). Bear Valley Road was built by filling in and diking the marshes at the confluence of Bear Valley Creek and Lagunitas Creek. Additionally, the construction of the Levee Road changed a salt and brackish water marsh into a largely freshwater marsh (TBA, 1994). In 1873, a large amount of earth was removed from where Silverhills Road is now, and the ¾-mile long Levee Road was built along with three wooden bridges (TBA, 1994). Sir Francis Drake Boulevard runs the length of the Lagunitas Creek watershed. Sir Francis Drake was built sometime after 1892 and transects many tributary streams in addition to mainstem Lagunitas Creek, and has resulted in many stream crossings throughout the watershed and along the west shore of Tomales Bay (Niemi and Hall, 1996). Highway 1 runs from the southern to the northern end of the watershed and also transects Lagunitas Creek, many tributary creeks and Walker Creek along its length.

4.0 Mariculture “We need to think and act as the very important part of the watershed that we are- not as separate observers- because we have the power to do so much harm or good. Knowing that, we should step lightly, use wisely, and help others to do the same.” -- John Finger, Tomales Bay mariculturist

Mariculture can be envisioned as the conjunction of agriculture and the marine environment. Oyster farming- the primary focus of mariculture on Tomales Bay- is the practice of animal husbandry where hatchery-raised oyster “seed” or spat are placed in the marine ecosystem to grow until harvest for market. Mariculture leases on the bay bottoms are administered by the California Department of Fish and Game (CDFG), which determines where leases shall be sited, the species that are permitted to be grown on the leases, and is ultimately responsible for assuring that mariculture operations do not critically impact or compromise the health of the ecosystem. The safety and quality of these farm products as foodstuffs are closely monitored by the DHS. Commercial oyster production in Tomales Bay is a testament to the

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relative cleanliness and health of the ecosystem; Tomales is one of only four estuaries in California to be legally certified by the DHS as suitable for oyster farming. In 1875 mariculture began on Tomales Bay when a shipment of eastern oysters was planted near Millerton Point. Early mariculture operations included the Pacific Oyster Company (1907) and the Tomales Bay and Jensen Oyster Companies, both established in 1913. Increasing levels of pollution in San Francisco Bay brought an end to their oyster industry by the late 1930’s and the demand for oysters grown in Tomales Bay subsequently increased. By the 1950’s Tomales Bay was the largest producer in the State, accounting for 79 percent of the total harvest before leveling off to 18 percent of the total by 1993. The Pacific oyster (Crassostrea gigas) from Japan was introduced to California when it was planted in Tomales Bay in 1928 by the Tomales Bay Oyster Company. Hardier, faster growing, and better suited to the relatively cool waters of this region of the Pacific Ocean, the Pacific oyster has become the mainstay of the local mariculture industry. Lesser amounts of another Japanese species, the Kumomoto (C. gigas kumomoto) and the Eastern (C. virninica) oyster are also farmed. As the Japanese and Eastern oysters will not naturally reproduce in the cold waters of Tomales Bay, they can be considered ideal aquaculture species as their populations within the bay can be fully managed. Other maricultured species include Manila clams (Tapes semidecussata) and mussels (Mytilus edulis and M. galloprovincialis). In the 1990’s there were some attempts to farm-raise abalone (Haliotis rufescens) in the Bay, but the seasonal plunges in salinities during high rainfalls and the associated mortalities would suggest that this species is not viable for mariculture in Tomales Bay. Currently abalone is not a permitted species on any of the mariculture leases. From a land-use perspective, mariculture operations take up a small percentage of the bay’s total acreage. Natural boundaries, such as tidal constraints, as well as regulatory boundaries, such as protected eelgrass beds and navigational right-of-ways, all restrict the feasible growing area in the bay. Currently, six leasees hold twelve leases totaling 513 acres; of this total approximately 135 acres are actually footprinted by mariculture operations (Moore, 2002). The shellfish growing areas of Tomales Bay have been given conditional approval by DHS due to concerns over microbial contamination. The purpose of the conditionally approved classification is to provide a mechanism for the declaration of harvest closures during periods when the growing areas does not meet National Shellfish Sanitation Program (NSSP) standards for harvesting shellfish for direct marketing for human consumption. In Tomales Bay these periods when harvesting shellfish are suspended occur during significant rainfall events (0.4 inches to 0.6 inches) within a 24-hour period. In the winter months, harvest and sales of shellfish can be restricted for prolonged periods. In 1993 the Shellfish Protection Act was created by the State in an attempt to improve water quality by mandating the creation of a Tomales Bay Shellfish TAC to assess water quality issues, and to develop recommendations to effect water quality improvements. Mariculture can be both beneficial and detrimental to the ecosystems of Tomales Bay. The beneficial effects of oyster cultivation include the filtration of bay waters that both increases Tomales Bay Watershed Stewardship Plan: A Framework for Action 43

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water clarity and benefits ecosystems such as the eelgrass beds. Oyster beds also provide habitat for a variety of marine species. But “creating” habitat often displaces habitat and the species that depend on it. Mariculture operations encroach on the natural bay habitat and can disrupt those ecosystems. For example, research conducted in the tidal flats of Tomales Bay suggests that the two most abundant shorebird species on the bay, the western sandpiper and dunlin, avoid foraging in mariculture areas (Kelly et al., 1996). Other potential negative effects of mariculture include the introductions of non-native species and diseases. These risks are increased by the practice of purchasing mature shellfish from elsewhere and holding them in the waters of Tomales Bay for eventual resale. Unlike the seed oysters that come from the controlled environment of a hatchery, adult oysters brought in from other open marine systems are more likely to be hosts for diseases and unwanted hitch-hiker species. In the broad overall picture, mariculture demands our attention to water quality. Mariculture does not so much raise the standards of water quality as it raises the regulatory and stakeholder focus on active management. Mariculture provides the need for ongoing water quality monitoring of growing waters, the need for programs like the Shellfish TAC, and an incentive to both protect and improve our current high level of water quality.

5.0 Recreational Uses “The Tomales Bay watershed’s abundance and beauty fed the bodies, spirits, and souls of the native people for thousands of years. The protection and appreciation of these irreplaceable natural resources is a responsibility that we all need to share for the benefit of generations to come.” -- Carlos Porrata, California State Parks Western Marin County has been a long-time favorite recreational destination, especially for San Francisco and other Bay Area residents. The Tomales Bay watershed offers opportunities for a wide variety of recreational activities in federal, state and county parks and at numerous private facilities. Recreational uses of the watershed include hiking, camping, kayaking, bird watching, swimming, boating, fishing, clamming, hunting, gathering, bicycling and horseback riding. Visitation to this area has increased significantly in the last several decades, and more than 2.5 million visitors come to this area annually (County of Marin, 1981; National Park Service, 2001). Boating and kayaking. Tomales Bay is a popular place for boaters of all types. The most common uses include kayaking, sport fishing and sailing. The Inverness Yacht Club was founded in 1912 and their charter identifies stewardship of the bay as one of their enduring responsibilities. The PRNS has permitted eleven kayaking companies as commercial operators on Tomales Bay. These companies operate day tours, overnight trips and classes in addition to offering kayaks for hire throughout the year. Commercial passenger fishing vessels from Bodega Bay regularly fish in Tomales Bay.

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Equestrian facilities and horseback riding. Horseback riding, horse stables and equestrian facilities are common throughout the Tomales Bay watershed. In 2001, there were 3,381 horses in Marin County (Benito and Sundin, 2001). These horses are kept by individuals and in commercial boarding stables on both private and public lands. In addition, an unknown number of horses are brought in by visitors to use trail systems in many of the parks, open space areas and on private lands. Camping. Wilderness camping occurs along the western shore of Tomales Bay, where the majority of areas are accessible only by boat. Camping by kayak along this western shore has significantly increased in popularity in recent years. As a result, the NPS has established a permitting program for camping on some of the bay’s beaches. Two of these beaches, Marshall and Tomales Beaches, provide waste receptacles. No facilities for waste disposal are available at other beaches, and users must pack out garbage and human waste. Fire permits are required. Car camping is available at Samuel P. Taylor State Park, Olema Ranch Campground and Lawson’s Landing. Lawson’s Landing is the largest of these facilities and one of the older private resorts in the Tomales area, and includes 1,000 campsites, 233 permanent trailer sites, unlimited day use, boat storage and launching, clamming, fishing, hiking, and picnicking. Hiking and biking. There are numerous areas throughout the watershed with hiking and biking trails on federal, state and county lands. These trails can be found in the PRNS, GGNRA, Samuel P. Taylor State Park, Tomales Bay State Park, Millerton Point, Tomasini Point, among many other locations. In addition to these trails, the roads of West Marin are popular weekend destinations for cycling teams and bike riders during most of the year. Hunting and gathering. While utilizing the natural resources is no longer essential for survival for humans in the watershed, both residents and visitors take advantage of the intrinsic natural abundance of the area. Hunting is legal on both private lands and the waters of Tomales Bay. On the bay, hunting for ducks and geese is concentrated near the mouths of Lagunitas and Walker creeks, two large areas of marsh habitat (Kelly and Tappen, 1998). On private property in the watershed hunting is primarily focused on deer, ducks over small water impoundments or “duck ponds,” and occasionally on quail and other small game. Hunting is regulated by the CDFG and is not permitted in the national, state or local parks. Firewood is still gathered extensively in the watershed. In the late 1800’s the production of firewood was one of the major industries in the watershed (Alley, Bowen and Co., 1880), but current levels of harvest are predominantly limited to fire control, road maintenance and the opportunistic use of windfalls. Wild mushrooms, berries, herbs, and a remarkable assortment of flora are gathered throughout the watershed. Watercress is found in small streams. Nettle leaves are picked and used in the commercial production of a type of local cheese. Edible seaweeds are found along the shoreline of the bay and collection is under the jurisdiction of CDFG. In state and federal parks, collection of the more commonly pursued flora - mushrooms and berries - is managed by established limits and other restrictions. Tomales Bay Watershed Stewardship Plan: A Framework for Action 45

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Fishing. Please see Section 7.0 for a discussion of commercial and recreational fishing.

6.0

Open Space 6.1

Non-agricultural open space

Non-agricultural open space in the Tomales Bay watershed can be found mostly within the Lagunitas Creek watershed area. Approximately 40 percent of the Lagunitas Creek watershed is open space, including: 20,000 acres that are owned by MMWD; a 42 acre wildlife preserve on Olema Marsh owned by ACR; the 2,010 acre Samuel P. Taylor State Park; and six properties owned by the Marin County Open Space District, totaling approximately 2,040 acres (UCCE, 1995). MMWD owns about 30 percent of the watershed (mostly in the southern portion near the headwaters), and most of this property is not grazed except for small areas in the Nicasio Creek watershed (UCCE, 1995). MMWD also owns the watersheds of Alpine, Bon Tempe, Kent and Lagunitas Lakes. Walker Creek watershed non-agricultural open space lands include 20 acres at the confluence of Walker Creek and Keys Creek owned by the CDFG (UCCE, 1995). In addition, ACR owns most of the delta salt marsh where Walker Creek enters Tomales Bay. 6.2 Parks in the watershed Visitors to West Marin can enjoy a variety of recreational experiences in six federal, state and county parks. Agriculture and gathering are permitted on some of the parklands in the watershed, while hunting is prohibited. The PRNS and Tomales Bay State Park, together include approximately 50 percent of the 70 miles of shoreline in Marin County north of Bolinas, and provide most of the public access and recreational opportunities available in the watershed (County of Marin, 1981). Public lands with shoreline access to Tomales Bay include: PRNS; Tomales Bay State Park including Tomasini Point, Millerton Point and lands adjacent to Cypress Grove; Tomales Bay Ecological Reserve; and county parks Whitehouse Pool, Chicken Ranch Beach, and Miller Park. 6.2.1 Federal parks The Point Reyes National Seashore. The western parts of the Tomales Bay watershed lie within the PRNS on the Point Reyes Peninsula. This park encompasses 65,300 acres and includes ten beaches, 141 miles of trails and over 40 campsites in four locations. It offers various activities such as hiking, riding, camping, fishing and clamming. The PRNS has been a favorite recreational destination for many years, especially for residents of the San Francisco Bay and Sonoma County areas. Visitation to this park is over 2.5 million per year. Golden Gate National Recreation Area. Together with the PRNS, the GGNRA owns 14,122 acres in the Lagunitas Creek watershed and 8,925 acres in the Olema Creek

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watershed (UCCE, 1995). Hiking, biking, and other recreational activities are permitted on lands owned by GGNRA. 6.2.2 State parks State parks include lands along the eastern and western shores of Tomales Bay, a significant area within the Lagunitas Creek watershed, Millerton and Tomasini Points, Marconi Conference Center and Marconi Cove. Recent acquisitions on the eastern side of Tomales Bay have expanded the Millerton Point and Tomasini Point parcels across Highway 1 and further up into the watershed. Samuel P. Taylor State Park. Samuel P. Taylor Park is visited by approximately 100,000 tourists a year. Visitors picnic, hike, bike, swim, camp and ride horses through the park’s picturesque trails, trees and creeks. The creeks that flow through the park are a significant attraction for visitors. Equestrians and hikers can also be seen along creek-side trails. The old logging railroad bed along the creek from the old mill site to Tocaloma is now a recreational trail. Tomales Bay State Park. The main body of the park includes nearly 2,400 acres, 3.5 miles of bay shoreline, four beaches, a picnic site, and 4.5 miles of trails. Annual visitation to the Park is approximately 124,000 people. Additional acquisitions to Tomales Bay State Park include 1,200 acres west of Inverness with limited public access on fire roads, Tomasini and Millerton Points and 22 acres adjacent to Cypress Grove on the east side of Tomales Bay. Tomasini and Millerton Point parklands cover 420 acres with 2.7 miles of shoreline on the bay. The park allows public access for hiking, observing wildlife, clamming, boating, picnicking, fishing, and viewing. 6.2.3 County parks Chicken Ranch Beach. This small park includes four acres of beach and marshland, and is located on the west side of Tomales Bay. It is a popular beach used by residents and visitors for walking, picnicking, sunbathing, and swimming. Whitehouse Pool. Whitehouse Pool is a 23.5 acre-park along the tidal reaches of Lagunitas Creek, at the confluence with Olema Creek, and is commonly used for creek access by kayakers and canoers, hiking and bird watching. Miller Park. Miller Park is a six-acre, day use facility adjacent to Nick’s Cove, on the east side of Tomales Bay. The park has 730 feet of shoreline frontage and has been developed with a boat launch, pier, picnic tables, restroom facilities, and a parking area. This park is a popular recreational area and receives heavy use by the public for boating, clamming, kayaking and fishing (County of Marin, 1981). Open Space. Marin County Open Space District owns the Gary Giacomini and French Ranch Open Space Preserves, providing over 2,000 acres of hiking, biking and equestrian recreation. Tomales Bay Watershed Stewardship Plan: A Framework for Action 47

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6.2.4 Other parks The Inverness Foundation owns four small parks within the village of Inverness, namely: Dana Marsh. This marsh is a small strip, about one acre, just south of the Golden Hinde Hotel, between Sir Francis Drake Blvd. and the bay, and supports a great variety of plants and animals. 2nd Valley Nature Preserve. This 3.68-acre preserve has a creek running through it, and the majority is kept in a natural state. The Inverness Tennis Club uses about ½ acre for its court, on a lease arrangement, but otherwise it is undisturbed. Martinelli Park. This park is a strip of 7.2 acres, although more than half of it is normally under water, extending from the parking lot of the Inverness Store along the edge of the bay. Martinelli Park is visitor-oriented with a couple of benches and restrooms. It also serves as a helicopter pad when emergencies arise. Plant Park. This 9-acre park extends from Sir Francis Drake Blvd., just south of the Bellweather and Post Office building, inland for 9 acres. It contains a natural garden, cared for by community volunteers, several picnic tables, apple trees, and the farthest inland portion is in a natural state. 6.3 Reserves Audubon Canyon Ranch. ACR was founded in 1962 to preserve, protect and manage lands as sanctuaries for native plants and animals in Marin and Sonoma counties. ACR has numerous land holdings within the watershed primarily along the Tomales Bay shoreline and in the marsh areas of Lagunitas and Olema creeks. ACR has a reserve of 139 acres on the bay at Cypress Grove, with approximately 250 acres of additional lands that include Walker Creek delta, Tom’s Point, and several other shoreline areas around the Bay. Significant holdings also include Olema Marsh and Shield’s Marsh. Tomales Bay Ecological Reserve. The Tomales Bay Ecological Reserve is owned by the State of California under the State Lands Commission, and is located south of Millerton Point at the end of Tomales Bay. The reserve, with about one mile of shoreline frontage, includes almost 500 acres of marsh used by migrating waterfowl and other wildlife. Public access to the reserve is possible at various points and the reserve is primarily used for duck hunting.

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7.0 Fisheries For thousands of years man has benefited from the remarkable natural abundance of aquatic organisms found in Tomales Bay and its tributaries. Coastal Miwok found a significant portion of their diet on the diverse array of mollusks, crustaceans, and fishes that were available. Early European settlers found accessible populations of bivalves and salmonids as well as vast populations of herring, sardines, and other small fishes of the bay. As the regional populations grew, subsistence-based fishing evolved into the division between recreational and commercial fishing that is the existing guideline today As human impacts on both aquatic organisms and their habitats have grown, the populations of a number of aquatic species have apparently decreased. Little information exists on the populations of bay or coastal fish and invertebrate populations, and only those with strict legal protections (e.g. endangered coho salmon) or a perceived economic basis (e.g. Pacific herring) are provided with any degree of population monitoring by regulatory agencies. Local, regional, and coastal populations have been significantly altered by over-harvesting associated with fisheries; habitat degradation in both freshwater and marine ecosystems; water quality degradation and hydrologic modifications; oceanic conditions; and other variables. Tomales Bay once supported large coho salmon and steelhead trout fisheries. State and Federal Endangered Species Act (ESA) guidelines have completely closed these fisheries (except for the catch and release of steelhead in the tidal reach of Walker Creek). Fishing on all tributaries of the watershed is now restricted to the waters upstream of the six major MMWD water impoundments (CDFG, 2002). Anecdotal evidence suggests the steep declines in the populations of white sea bass, striped bass, starry flounder, diamond turbot, pacific sardine, and pacific littleneck clam in modern times. Some, like the Pacific sardine and white sea bass, are transient and have been reappearing as their relative abundance on the coast has grown (Leet et al., 2001). 7.1 Commercial fisheries The primary commercial fishery in Tomales Bay is Pacific herring (Clupea pallasi), an oceanic fish related to the sardine which groups into large schools in the winter and migrates to spawn in the bay. This fishery began in the 1870’s as San Francisco’s herring populations were already being depleted (Suer, 1987). Consumer taste, market forces, and abundance levels cause large fluctuations in the early fishing efforts for herring. Changes in the world herring market brought substantial Japanese demand on the herring populations in north central California. The modern herring fishery is almost exclusively for the Japanese herring roe market. The fishery is a limited-entry gillnet program that targets egg-bearing females as they congregate to spawn. Catches in the Tomales Bay herring roe fishery have ranged from a high of 871 tons in 198687 to a low of zero tons in 1997-1998 (CDFG, 1999). High catchment rates in the late 1980’s and the subsequent low biomass observations at the end of the decade caused CDFG to close the fishery for three years. Since its re-opening, fisheries managers have established Tomales Bay Watershed Stewardship Plan: A Framework for Action 49

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quotas based on a combination of the previous year’s spawning biomass and the current year’s estimated abundance; quotas are approximately 15% of the spawning biomass estimate with a 20% maximum. Since the 1989-1990 closure of the fishery, catches have been within these ranges (Leet et al., 2001). Herring stocks are subject to fluctuations that result from a variety of conditions including, El Ninos, drought, oceanic productivity, water quality, and over-fishing (National Park Service, 2001). Lesser commercial fisheries in Tomales Bay include halibut, perch and live-bait. The commercial halibut fishing effort is modest and opportunistic, generally associated with periods of relative high abundance and/or with limitations or closures of other commercial fisheries, such as salmon. Reporting on commercial halibut landings is inadequate to provide practical estimates on the Tomales Bay commercial halibut harvest (National Park Service, 2001). A small number of commercial fishermen occasionally take perch and a nascent livebait fishery targets anchovies and sardines for sport fishing operations in Bodega Bay. Some agencies and residents have expressed the concern that the incidental bycatch of the live-bait fishery could impact the juvenile populations of salmonids and rockfish (National Park Service, 2001). CDFG, the primary agency with jurisdiction over fisheries regulations (various federal and water district agencies contribute the rest), has significantly limited some of the commercial fisheries in Tomales Bay. Restrictions include the closures of both the very north and south ends of the bay to all commercial fishing, an exclusion of all set gear (longlines), and the prohibition of the use of power-driven pumps or hydraulics in the extraction of benthic species like ghost and mud shrimps (Cal. Code Reg. title 14 §120.6). 7.2 Recreational fisheries The recreational halibut fishery attracts the largest number of anglers to Tomales Bay; peaking during the summer months, over 200 boats/day have been counted while other anglers fish from the shoreline. In an effort to quantify the fishing effort and to begin to understand the bay’s halibut populations, CDFG and a number of volunteers began in 1995 to conduct a volunteer creel census and halibut tagging program where the movements of halibut are documented through tag returns on re-capture. Horseneck (gaper) clamming draws thousands of recreational users out onto the bay’s northern shoals during extreme low tides. CDFG estimates that annually 55,000 clams are taken by as many as 1,200 people per day on peak weekends (Leet et al., 2001). Washington clams, the smaller Pacific littlenecks, and the non-native manilas are also taken. CDFG has speculated on the apparent declines in the populations of these smaller clams, citing the influences of agricultural runoff, septic material, sediments, and above-average rainfall (Leet et al., 2001). Other recreational fisheries in the bay include Dungeness and rock crabs, jacksmelt, perch, sole, striped bass, sturgeon, sharks and rays. In the late 1990’s, tissue samples from some of the most commonly taken species were analyzed for toxins and in 2000, the Marin County Department of Health and Human Services (MCDHHS) issued a health advisory and Tomales Bay Watershed Stewardship Plan: A Framework for Action 50

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recommended consumption levels for sport-caught halibut, perch, smelt, sharks, and rays because of detected mercury levels (MCDHHS, 2000).

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Literature Cited Alley, Bowen and Co. 1880. History of Marin County, California. Benito, C. A. and K. R. Sudin. 2002. The Economic Value of the Marin Equestrian Sector. Sonoma State University, California. Bush, Lisa. 2003. Personal communication. Range management and agricultural consultant, Santa Rosa, California. Burcham. L.T. 1957. California Range Land. State of California Department of Natural Resources, Division of Forestry, Sacramento, CA. 256 pp. California Code of Regulations Title 14 §120.6. California Department of Fish and Game (CDFG). 2002. Sportfishing Regulations Booklet. CDFG. 1999. 1997-1998 Commercial Fish Landing Records. California Division of Mines and Geology (CDMG). 1972. Basin Planning Study, Principal Areas of Mine Pollution. California Water Resources Control Board California Regional Water Quality Control Board. 1995. San Francisco Bay Basin (Region 2) Water Quality Control Plan. California Regional Water Quality Control Board, San Francisco Bay Region. 167 pp. County of Marin. 1981. Marin County Local Coastal Program, Unit II. Adopted by the Marin County Board of Supervisors (December 1980) and Certified by the State Coastal Commission (April 1981). Edwards, S.W. 1992. Observations on the prehistory and ecology of grazing in California. Fremontia 20(1):3-11. Evens, J.G. 1993. The Natural History of the Point Reyes Peninsula. Revised Edition. Point Reyes National Seashore Association. 224 pp. Kay, J. 2000. Tainted Tomales. Article in the San Francisco Examiner. 1/9/00. Kelly, J. P. and S. L. Tappen. 1998. Distribution, Abundance and Implications for Conservation of Winter Waterbirds on Tomales Bay, California. Western Birds 29:103-120. Kelly, J.P., J.G. Evens, R.W. Stallcup, and D. Wimpfheimer. 1996. Effects of aquaculture on habitat use by wintering shorebirds in Tomales Bay, California. Calif. Fish Game 82(4):160-174. Leet, W.S., Dewees, C.M., Klingbiel, R. and E. J. Larson (eds.), California's living marine resources: a status report, p. 334-335. ANR Publ. SG01-11. Calif. Dep. Fish Game and Univ. Calif. Agric. Nat. Res. Marin County Department of Health and Human Services (MCDHHS). 2000. Interim Health Advisory for Sport Fish From Tomales Bay. November, 2000. Moore, Tom. 2002. Personal Communication. Re: Unpublished Tomales Bay environmental documentation on the Tomales Bay Mariculture Program. California Department of Fish and Game, Bodega Bay, California. National Park Service. 2001. Tomales Bay: Guidelines for Protection and Use. Point Reyes National Seashore. Point Reyes Station, CA. 33 p. Niemi, T.M. and N.T. Hall. 1996. Historical changes in the tidal marsh of Tomales Bay and Olema Creek, Marin County, California. J. Coast. Res. 12:90-102. Press, David, National Park Service, pers. comm. 2001. Point Reyes National Seashore. PRNS (Point Reyes National Seashore, NPS). 2001. Water Quality Monitoring Report May 1999-May 2001. Tomales Bay Watershed Stewardship Plan: A Framework for Action 52

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Shannon and Associates. 1997. Lawon’s Landing Master Plan. Dillion Beach, California. Suer, A. L. 1987. The Herring of San Francisco and Tomales Bays. Ocean Research Institute, San Francisco. 64 pp. Thurber, S. 1970. Healing a mining operation’s scars. Article in San Francisco Chronicle. 11/26/70. Treganza, Adan E. Unknown. The Indian Story of Point Reyes. Tomales Bay Association (TBA). 1994. Tomales Bay Watershed – Fall Newsletter. Tomales Bay Association, Point Reyes Station, California. Tuden, Rebecca. 2002. Personal Communication. University of California Cooperative Extension (UCCE). 1995. The Marin Coastal Watershed Enhancement project. University of California Cooperative Extension. Novato, California. 83 pgs. Whyte, Dyan. 2003. Personal communication. San Francisco Regional Water Quality Control Board. Whyte, D. C. and J. W. Kirchner. 2000. Assessing water quality impacts and cleanup effectiveness in streams dominated by episodic mercury discharges. In The Science of the Total Environment 260: 1-9. Whyte, D.C. and P.M. Ganguli. 2000. The impact of mercury mining on Tomales Bay biota. EPA mercury conference. Zumwalt, C. W. 1972. Consideration of vegetation and soils on the Tomales Bay Watershed. In Tomales Bay Environmental Study, (Ed.) Corwin, Ruthann., Washington D.C.: The Conservation Foundation.

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III. A FRAMEWORK FOR WATERSHED STEWARDSHIP These goals are intended to guide future programs and projects, and to assist funding organizations in ascertaining our needs at the watershed scale. These goals drove the development of the Action Plan, which identifies high, medium and low priority activities in the Tomales Bay Watershed Stewardship Plan.

A. GOALS AND OBJECTIVES Goal A. Ensure water quality in Tomales Bay and tributary streams sufficient to support natural resources and sustain beneficial uses (as defined in the attached glossary). Objective 1: Improve water quality in Tomales Bay and tributary streams through reductions in sediment, pathogens, mercury and nutrient loading - with the specific objectives of protecting all beneficial uses, and removing Tomales Bay from the 303(d) list of impaired waterbodies by attaining state and federal water quality standards. A benchmark for success in reducing pathogen levels will be a reduction in shellfish harvest closures by increasing the rainfall threshold and reducing the minimum duration of shellfish harvest closures. Benchmarks for sediment, nutrients and mercury will be developed as regulatory agencies further develop reduction plans for these pollutants. Objective 2: Restore and maintain adequate high quality freshwater flow to Tomales Bay and tributary streams. Objective 3: Reduce potential for other contaminants in Tomales Bay. Goal B. Restore and preserve the integrity of natural habitats and native communities. Objective 1: Restore and protect populations of native species in the Tomales Bay watershed. Objective 2: Control invasive non-native species in the Tomales Bay watershed. Objective 3: Restore and protect habitats of native species in the Tomales Bay watershed. Objective 4: watershed.

Restore and protect the hydrologic integrity of the Tomales Bay

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Goal C. Develop strategies to implement the Plan and to protect the watershed. Objective 1: Encourage comprehensive planning to address watershed issues and facilitate interagency coordination and cooperation. Objective 2: Monitor implementation of this plan. Develop recommendations for public policies and programs to achieve the goals of the Plan. Objective 3: Define the role of the Council in helping to ensure implementation and achievement of Plan goals. Objective 4: Involve and educate the public to become watershed stewards.

B. ACTION PLAN “[It] is our privilege as residents of this watershed, working together to strengthen the place we share. And this work is our most valuable legacy for those who will follow us.” -- Michael Mery, Point Reyes Station The Action Plan defines activities needed to achieve the goals of the Watershed Stewardship Plan. These activities may be undertaken voluntarily, and we have identified lead and supporting partners for each task and we look to those entities to act. Some of the recommended actions are already being implemented, while others have yet to be initiated. The Council will support implementation of this Plan, taking on specific programs and projects that are beyond the mission or capacity of individual organizations/agencies or established partnerships. The Council will also continue to provide a forum where programs and projects are discussed and evaluated. Prunuske Chatham, Inc. provided preliminary cost estimates as a starting point in the development of future proposals, some of which appear in Appendices A and B. At this time, there is sufficient information to undertake many appropriate management and restoration actions through implementation of the recommendations contained in this Plan. In the future, additional assessment will be useful in guiding us towards more effective and efficient policies and programs; however, due to the complex nature of this natural system, we will continue to depend on the best available information and professional judgment if our efforts to manage human impacts on this system are to be timely.

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Action 1.0 Develop a coordinated and comprehensive water quality monitoring plan for Tomales Bay and tributary streams. Clean water is essential to aquatic, coastal and marine environments. In the Tomales Bay watershed, water quality and healthy aquatic habitats are influenced by tidal circulation, by activities that occur nearby on land, and by pollutants delivered via surface run-off and subsurface seepage. A comprehensive long-term monitoring program is needed to document baseline conditions and identify trends for pollutants of concern. Pollutants refers to human created or induced alterations in the physical, biological or chemical character of water thereby producing undesirable environmental results, as well as the standard evaluation of substances effecting human health. Monitoring would provide the information needed to evaluate water quality in the bay and its tributaries, as well as the efficacy of projects to reduce non-point sources of pollution, management practices intended to improve water quality, and educational programs. It is anticipated that considerable energy and capital will be expended to improve water quality and it is essential to have a scientifically valid database to determine action efficiency. In this way, adaptive management and conservation strategies based on the most current and best available monitoring data can be incorporated into future actions in the watershed to improve water quality and watershed health. The development of a comprehensive water quality monitoring program is only the first step in watershed monitoring for Tomales Bay. Along with baseline monitoring (to characterize existing conditions) and effectiveness monitoring (to determine the success of existing or newly implemented projects or management practices), bio-indicators should be identified and monitored. Lists of monitoring and assessment recommendations are included in Appendix A: Water Quality Status and Trends Report, and Appendix B: Erosion and Sedimentation in the Tomales Bay watershed for consideration in the development of a comprehensive water quality monitoring plan. In addition, it is necessary to monitor and evaluate land-use practices and other human influences on tributaries to the bay, uplands, riparian corridors, wetlands and along the bay shores. Voluntary landowner monitoring will provide important information about the effectiveness of projects on private lands. Together, these monitoring activities will provide the framework for adaptive management, which will increase the effectiveness of our actions. Some components of this program can be carried out by existing agencies if the components fit into an agency’s specific directives and goals. Others will need to be carried out by organizations outside the regulatory network (such as academic institutions and non-profit groups). However, without a central group to coordinate activities, monitoring efforts will continue to serve specific goals rather than lead to an overall understanding and improvement in the health of Tomales Bay. The Bay Institute, which oversees and coordinates a long-term water quality monitoring program for San Francisco Bay, or the Morro Bay and Tillamook Bay National Estuary Programs, could be used as a model for such a group. Purpose: • Obtain high quality baseline data describing the concentrations of contaminants in the waters of Tomales Bay and tributary streams, and to increase understanding and awareness of water quality problems in the watershed. Tomales Bay Watershed Stewardship Plan: A Framework for Action 56

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• • • •

•

• •

•

Measure effectiveness of management practices implemented on public and private lands to reduce sediment, bacteria and nutrient delivery, and other non-point sources of pollution. Increase understanding of water quality problems in the watershed including the impacts of septic systems, sewage ponds and landfills on the water quality of Tomales Bay and tributaries. Identify temporal and spatial changes in the bay and tributary streams. Determine seasonal, annual and long-term trends in chemical, physical (e.g. sedimentation), and bacteriological water quality in Tomales Bay and the tributary streams. Determine whether water quality, and sediment contamination and supply, in Tomales Bay and tributary streams are in compliance with objectives established in the San Francisco Bay RWQCB’s Basin Plan, Marin Countywide Plan, Local Coastal Program, Shellfish Protection Act, etc. Provide adequate information and recommendations to result in water quality improvements to reduce shellfish harvest closures during winter rain events by reducing run-off containing high concentrations of coliform bacteria. Evaluate and revise minimum required closure period for shellfish grown in Tomales Bay based on data. Provide a database on water quality that is compatible with data being developed in ongoing studies in Tomales Bay and tributary streams. Provide a clearinghouse and monitoring database for use by landowners, stakeholders, regulatory agencies, watershed managers and the general public through such media as the Internet (web page), published reports and readily available, computer searchable databases. Provide volunteer monitoring opportunities for local communities and schools

Lead: The Tomales Bay Watershed Council, via its Water Quality Committee, will be the lead in the development of this Water Quality Monitoring Plan. Core group of program partners: California Department of Health Services, Regional Water Quality Control Board, Marin County Environmental Health Services, U.C. Cooperative Extension, Salmon Protection and Watershed Network, Tomales Bay Agricultural Group, Tomales Bay Shellfish Technical Advisory Committee, Gulf of the Farallones National Marine Sanctuary, California Department of Fish and Game, Pacific Coast Learning Center, Point Reyes National Seashore, Point Reyes National Seashore Association, Tomales Bay State Park, shellfish growers, Marin Municipal Water District, Inverness Public Utility District, North Marin Water District, U. S. Geological Service, U.S. Environmental Protection Agency, ranchers, private landowners and local non-governmental organizations.

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I. High priority, short-term activities for developing a coordinated and comprehensive water quality monitoring plan for Tomales Bay and tributaries. Please note that some of these activities are interrelated and do not necessarily to occur in this exact order. See reference year following each step. •

Purpose: Define the purpose and identify the questions to be answered with this monitoring plan. (2003) Cost estimate: $5,000

•

Status: Summarize historic and current water quality monitoring efforts and data. Collect data on sources of pollution, and develop initial database. Identify pollutants of concern and water quality problems in Tomales Bay watershed. (2003). Cost estimate: has been initiated using planning funds

•

Trends: Identify trends, based on historical and current data. (2004). Cost estimate: $15,000

•

Regulatory status: Determine which agencies have regulatory responsibility for development of best management practices, specific contaminant monitoring, enforcement of the Clean Water Act, etc. Identify actions already taken by those agencies. (2003-2004). Cost estimate: $5,000-10,000

•

Prioritize: List and rank known and potential sources of pollutants of concern. (2003-2004). Cost estimate: $5,000-10,000

•

Fill data gaps: Identify gaps in existing data and incompatibilities between databases. Decide how to fill data gaps. (2003-2004). Cost estimate: $5,000-10,000

•

Develop a water quality and quantity monitoring plan: The plan should identify the questions to be answered, outline the approaches to take, describe the limitations, estimate the costs, and develop a sampling plan. The plan is likely to include monitoring to develop a baseline, to support existing actions (e.g. development of a TMDL), and to evaluate current monitoring tools and methods, and the implementation of remediative actions. The plan shall identify lead(s) for implementation, and have an adaptive management component. (Start 2003-2004, ongoing for the life of the monitoring program). Cost estimate: $90,000

•

Database: Continue development of the database stated under Step 2 that will allow for long-term trend analysis. Design a framework to support maintenance and updating of database. (Start in 2003, on-going for the life of the program). Cost estimate: $35,000

•

Funding: Work with leads to identify and secure adequate funding for equipment, monitoring and sampling, staffing and related needs. (Begin 2003, on-going for the life of the monitoring program). Cost estimate: $15,000

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•

On-going coordination: Identify a central organization to coordinate existing water quality monitoring efforts going on in the watershed and to serve as a “clearinghouse.” (Begin 2003, on-going for the life of the monitoring program). Cost estimate: $40,000 per year

•

Implementation and analyses: Facilitate implementation of the monitoring program and support on-going efforts. Analyze trends. Develop recommendations for actions to improve water quality. (Implement the water quality monitoring program in 2004, on-going for the life of the program). Cost: unknown at this time

•

Indicator Species and/or systems as a measure of water quality and overall “health” of the bay: Determine if there are resources to develop indictor species and/or systems for Tomales Bay. If so, the Council will work with technical advisors to identify indicators of watershed function. Thresholds and warning levels for indicators should be developed. (2004-2005). Cost: unknown at this time

These activities will be successful if they achieve these results. Specific criteria will be developed on a project basis: 1. Easy-to-use water quality database for Tomales Bay and tributaries. 2. Practical understanding of water quality problems, sources of pollution and primary loading routes to Tomales Bay and tributary streams by end of 2004. 3. Preliminary list of prioritized projects to reduce sources of contaminants by end of 2004. This list should be updated as the long-term monitoring program uncovers new information. 4. Recommendations for best management practices and restorative actions to improve water quality in Tomales Bay and tributary streams.

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Action 2.0 Support implementation of practices and projects that will reduce nonpoint sources of water pollution and enhance habitats in Tomales Bay and its watershed. During the past 20 years, significant steps have been taken on private and public lands to improve water quality and aquatic and terrestrial habitats in the Tomales Bay watershed. The momentum that has been created by partnerships between private landowners, local agencies and organizations has resulted in an increased understanding of water quality issues, the condition of Tomales Bay and tributary streams, and linkages between sources of pollutants and water quality. In addition, these activities have improved local awareness about native habitats in the bay and watershed. Future collaboration will be necessary to maintain this progress and to increase these local programs. Sources of water pollution in the Tomales Bay watershed include agricultural run-off with elevated levels of nutrients, sediment and bacteria; recreational activities and stormwater runoff that contribute pathogens and environmental toxins; groundwater contamination related to septic systems and storage ponds; and heavy metal pollutants from mines and marine facilities. BMPs are methods to control pollution sources and to maintain the integrity of a watershed ecosystem. BMPs offer private and public landowners the opportunity to change unsustainable management practices, and may preclude enforcement of environmental regulations by state and federal agencies. BMPs have been identified for road construction and grading; road crossings and culverts; septic system construction and maintenance; agricultural activities (including grazing, dairy operations, waste storage facilities, pasture fertilization, tilling and planting); mariculture; recreation; weed management; forest management and others. Most BMPs are subject to revision as research and experience lead to improvements, and as some practices become more technically or financially feasible (sometimes due to the availability of technical or financial support). When BMPs alone are not sufficient to protect water quality and sensitive habitats, it may be necessary to set limits on use. In many cases, private landowners who have implemented BMPs not only improved water quality, and riparian and aquatic habitats, they have also improved the economic viability/sustainability of their enterprises. For example, agricultural operators who collect and spread manure can reduce both potential sources of water quality contamination and the costs associated with fertilization and transportation of animal wastes. Similarly, implementing BMPs for culvert installation and road grading has resulted for many landowners in lower maintenance costs associated with poorly draining road surfaces and culvert failure. Future projects and programs to improve and protect water quality and habitats in the watershed will require the participation and collaboration of private and public partners. As with habitat restoration, water quality benefits accrue not only to local communities, but also to the millions of visitors that come to the watershed each year, to future generations to come, and to the many species for which the bay and watershed provide critical habitat.

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Future habitat restoration measures will require the on-going participation of and financial support for private and public landowners to implement best management practices. These management practices will include measures to reduce and contain the introduction and spread of invasive non-native species. During the next decade, the SWQCB and RWQCB will be developing TMDLs for pollutants of concern, and looking to local partnerships for assistance in implementing these plans to reduce water pollution. The continued support for and encouragement of community participation through voluntary management measures to resolve pollution problems will be a critical component to our success. These recommendations are intended to promote the protection of water quality and recognized beneficial uses of the bay and tributaries, habitats and species, and human health. Purpose: • Improve water quality and habitats in the Tomales Bay watershed. • Protect human health. • Benefit species of local interest (a list which will be developed by the Council) • Improve sustainability of human activities; including residential needs, agriculture, and mariculture. • Comply with local, state and federal laws and regulations. • Achieve regional and national water quality goals. I. High priority, short-term activities to reduce non-point sources of pollution and to improve aquatic habitats to be implemented and maintained: •

Implement projects to control livestock access to creeks as needed. Develop improved BMPs for animal waste management based on information derived from water quality monitoring programs on ranches and dairies. Partners: Marin Resource Conservation District, Natural Resource Conservation Service, property owners, Tomales Bay Agricultural Group, U. C. Cooperative Extension, Marin Agricultural Land Trust, County of Marin, State Coastal Conservancy

•

Support implementation, funding, and assessment of BMPs on agricultural lands, and in residential and commercial areas, especially where riparian and upland habitats may be affected. Partners: Tomales Bay Agricultural Group, U.C. Cooperative Extension, Marin Resource Conservation District, Point Reyes National Seashore, Regional Water Quality Control Board, Natural Resources Conservation Service, State Coastal Conservancy, California Department of Fish and Game, Marin Agricultural Land Trust, Marin County Building and Planning Depts., Marin County Dept. of Public Works, Tomales Bay Watershed Council

•

Provide adequate facilities to handle recreational sources of human waste. Partners: Point Reyes National Seashore, California State Parks, recreational users, Marin County, Interagency Group, Golden Gate National Recreation Area Tomales Bay Watershed Stewardship Plan: A Framework for Action 61

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•

Support community-based septic evaluation, improvement, management and monitoring programs. Consider alternative options for on-site treatment of human waste. Promote outreach, education and funding to achieve these programs. Include outreach to new homeowners, realtors, etc. Partners: East Shore Planning Group, Interagency Group, Department of Health Services, Marin County, Regional Water Quality Control Board, homeowners, Tomales Bay Watershed Council, Tomales Bay Shellfish TAC, Salmon Protection and Watershed Network, Coastal Conservancy, Village Associations

•

Improve and implement upland BMPs to reduce erosion, sediment and nutrient runoff, and to reduce and control the introduction and spread of invasive non-native species. Partners: landowners, National Park Service, California State Parks, Marin Resource Conservation District, Natural Resource Conservation Service, Tomales Bay Agricultural Group, U.C. Cooperative Extension, State Coastal Conservancy, Marin Municipal Water District, Marin County, SPAWN, Marin Agricultural Land Trust

•

Assess ecological effects of agriculture on Tomales Bay and its watershed, and support implementation of best management practices and related projects. Partners: Marin Resource Conservation District, Tomales Bay Agricultural Group, U.C. Cooperative Extension, Natural Resource Conservation Service, Marin County, State Coastal Conservancy, PRBO, Tomales Bay Watershed Council

•

Assess ecological effects of mariculture on Tomales Bay, and support implementation of BMPs and related projects. Partners: Department of Health Services, California Department of Fish and Game, aquaculture industry, U.C. Davis Sea Grant, San Francisco State University (Romberg Tiburon Center)

•

Assess ecological effects of recreational uses of Tomales Bay and its watershed, and support implementation of BMPs and related projects. Partners: Recreational outfitters, Point Reyes National Seashore, California State Parks, Department of Health Services, California Department of Fish and Game, Marin County, State Coastal Conservancy, Tomales Bay Watershed Council

•

Assess ecological effects of non-recreational uses of Tomales Bay, and support implementation of BMPs and related projects. Partners: Gulf of the Farallones National Marine Sanctuary, Coast Guard, Point Reyes National Seashore, Department of Health Services, California Department of Fish and Game, Marin County, Tomales Bay Watershed Council Tomales Bay Watershed Stewardship Plan: A Framework for Action 62

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•

Provide outreach and support to avoid future dumping of dirt into streams and wetlands along roads during county, state, federal and private road maintenance activities; and develop BMPs. Partners: Tomales Bay Watershed Council, CalTrans, National Park Service, landowners, Marin County, Pacific Gas & Electric Co., landscapers, construction workers, Salmon Protection and Watershed Network

•

Support additional funding for local organizations and agencies (e.g. Marin RCD, SPAWN, PRNS, TBA, Marin County, Trout Unlimited, and others) to implement projects consistent with the Council’s water quality and habitat goals and objectives. Partners: Tomales Bay Watershed Council and its member organizations and watershed partners

•

Develop and support enforcement of grading standards that better protect Tomales Bay. Partners: Marin County (Department of Public Works, Building Department), CalTrans, Regional Water Quality Control Board

•

Support educational efforts targeting road owners and managers about design, maintenance and management of roads to protect water quality. Educate homeowners, contractors and public agencies about erosion control and stream crossings. Partners: Tomales Bay Watershed Council, CalTrans, Marin County (Dept. of Public Works), property owners, Marin Municipal Water District, Salmon Protection and Watershed Network, Point Reyes National Seashore, Association of Bay Area Governments

•

Support County and State funding for a USDA Conservation Reserve Enhancement Program (CREP) to provide conservation easements for riparian area enhancement. Partners: Natural Resources Conservation Service, Tomales Bay Shellfish TAC, State Coastal Conservancy, Tomales Bay Watershed Council

•

Support programs to promote sustainable farming (e.g. the California Dairy Quality Assurance Program, Salmon Safe and Fish Friendly Farming). Partners: Marin Resource Conservation District, U.C. Cooperative Extension, State Coastal Conservancy, Tomales Bay Agricultural Group, Tomales Bay Watershed Council

•

Provide outreach to landowners and public agencies about importance of road construction and maintenance to minimize changes in natural runoff patterns. Support funding for improved road management. Partners: Marin Resource Conservation District, County of Marin (Dept. of Public Works, Planning Dept.), CalTrans, Marin Municipal Water District, National Park Service, Natural Resources Conservation Service, Salmon Protection and Watershed Network Tomales Bay Watershed Stewardship Plan: A Framework for Action 63

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•

Implement stream crossing best management and construction practices using hydrologic inventories and prioritization. Replace or maintain culverts to benefit salmonids, streams and wetlands. Partners: National Park Service, CalTrans, landowners, Marin County, State Coastal Conservancy, Salmon Protection and Watershed Network

II. Medium and long-term activities to reduce non-point sources of pollution and to improve aquatic habitats: •

Reassess and evaluate effectiveness of BMPs and projects implemented. priorities and recommendations based on this reassessment. Partners: Tomales Bay Watershed Council

•

Develop a management plan for recreational uses in the Tomales Bay watershed that impact water quality. Support implementation of these practices and related projects. Partners: Point Reyes National Seashore, California State Parks, Marin County, Tomales Bay Watershed Council, recreational users

•

Reduce water quality impacts of boating on Tomales Bay. Support implementation of these practices and related projects. Partners: Recreational users and outfitters, U.S. Coast Guard, California Department of Fish and Game, Gulf of the Farallones National Marine Sanctuary, California Coastal Commission, Marin County, National Park Service.

•

Manage water quality impacts of mariculture on Tomales Bay. Support implementation of these practices and related projects. Partners: Mariculturists, California Department of Fish and Game, Department of Health Services, Regional Water Quality Control Board, Gulf of the Farallones National Marine Sanctuary, U.C. Cooperative Extension

•

Identify regulatory agencies with jurisdiction in Tomales Bay and the watershed. Develop a watershed directory which includes contact information for relevant agencies and organizations. Partners: Tomales Bay Watershed Council, Strategies Committee

•

Promote interagency coordination for efficient issuance of environmental restoration permits. Lead: Marin Resource Conservation District Partners: Council, Marin County, Sustainable Conservation, Natural Resource Conservation Service, State Coastal Conservancy, JARPA

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Adapt

Associated cost estimates: Fencing $4.50/linear foot Construction of livestock water access $5,000-$10,000 each, includes design Stream crossings (not including bridges) $5,000-$8,000 each Rock headcut repair $120/ton placed Willow wall for stream bank stabilization $110/linear foot Brush mattress for streambank stabilization $135/linear foot These activities will be successful if they achieve these results. Specific criteria will be developed on a project basis: 1. Increased support and capacity for implementation of BMPs on private and public lands in the watershed. 2. Measurable improvements in water quality in Tomales Bay and tributary streams. 3. Measurable improvements in the health of terrestrial and aquatic habitats in Tomales Bay and its watershed. 4. Population growth in diminished native species. 5. Improved management and containment of invasive, non-native species.

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Action 3.0 Assess, protect and restore key habitats for species of local interest. Some species that are resident of or migratory through the Tomales Bay watershed are of particular local interest, though no comprehensive list of such species currently exists. Such a list might include native and non-native species, state and federally listed species, and species that are indicators of ecosystem health. In order to increase our understanding of the current condition and trends in the bay and watershed, such a list will be developed to provide a framework for monitoring fluctuations in these local populations. According to a recent report by the CDFG, exotic species, habitat destruction and fragmentation are the largest threats to the survival of endangered species (California’s Living Marine Resources: A Status Report, 2001). During the last two decades, projects on private and public lands to address habitat loss and degradation have lead to significant watershed benefits that include successfully reducing erosion rates and sedimentation of streams in parts of the watershed; neotropical migratory bird habitat enhancement; and increases in streamflows and aquatic habitat quality in lower Lagunitas Creek watershed. Although some habitats in the Tomales Bay watershed are relatively healthy, many have been seriously compromised and need to be restored. For example, the construction of large dams and reservoirs in the Lagunitas and Walker Creek watersheds has resulted in the loss of more than half of their historic spawning grounds for coho salmon and steelhead trout. Development, sedimentation, and destruction of riparian vegetation threaten what remains. Overall, little is known about the extent and distribution of invasive exotic species in the Tomales Bay watershed; however, some species or groups of organisms (e.g. rangeland plants) have been surveyed and efforts are underway to reduce their distribution and to improve containment. Today, more than 30 threatened and endangered species inhabit or migrate through the Tomales Bay watershed. It is estimated that over 10% of the annual wild coho salmon remaining in central California coastal watersheds use Lagunitas Creek and tributary streams for spawning and rearing, and local populations of the endangered red-legged frog are relatively strong. Walker Creek watershed supports steelhead trout and freshwater shrimp; however we do not know the size or significance of these populations. In addition, more than 600 native and endemic plant species have been identified on the Point Reyes Peninsula. Important populations of neotropical migratory birds also exist locally in riparian and coast scrub habitats. Future assessments will be necessary to guide and evaluate habitat enhancement activities. A list of assessment recommendations is included in Appendix B: Erosion and Sedimentation in the Tomales Bay as a starting point for future discussion about habitat assessment priorities. Voluntary protection of habitats on private and public lands has been critical in maintaining the diversity of the Tomales Bay watershed. Habitat restoration has been supported by local agencies using public funding to match the investments of private landowners. The policies in the Marin Countywide Plan and the Local Coastal Program have also supported the preservation of habitats and open space. As a result, significant restoration work has been Tomales Bay Watershed Stewardship Plan: A Framework for Action 66

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completed on private and public lands, and habitat improvement is being monitored. If these efforts are to continue, they will need the continuing financial and technical support of regulatory agencies and other organizations as well as political support within local communities. Habitat restoration should not only protect dependent species, but also maintain open spaces and protect critically sensitive areas for the overall health and function of the watershed. These recommendations are intended to define actions and programs the Council can implement or support to protect the Tomales Bay ecosystem. Purpose: • Benefit local species, including: endemic, threatened and endangered species, and other species of special concern. • Increase knowledge of local biodiversity and habitat needs to better manage and protect these species, and to improve understanding of locally extirpated species, • Support habitat conservation on private and public lands, and the implementation of sustainable management practices. • Monitor existing habitats and populations. • Monitor invasive, non-native species to guide management and containment. • Support inventories, continued and needed research for species of local concern to assess and document biodiversity and habitats within the watershed. I.

High priority, short-term activities to develop a habitats and species database.

Lead: In coordination with local scientists, the Tomales Bay Watershed Council will facilitate the creation of a program to collect, synthesize, analyze and guide and coordinate habitat assessment and restoration activities in the watershed. Core group of program partners: Point Reyes National Seashore, PRBO Conservation Science, Audubon Canyon Ranch, NOAA Fisheries, California Department of Fish and Game, State Coastal Conservancy, U.C. Davis and Extension, Bodega Marine Laboratory, U.S. Fish and Wildlife Service, S.F State University (Romberg Tiburon Center), Marin Conservation League, California State Parks, Marin Municipal Water District, Marin Resource Conservation District, Natural Resource Conservation Service, Salmon Protection and Watershed Network, Regional Water Quality Control Board, Gulf of the Farallones National Marine Sanctuary, local non governmental organizations and scientists. •

List: Develop criteria and create a list species of local interest. Cost estimate: $5,000

•

Database: Facilitate consolidation of existing information on distribution and abundance of species of local interest in the watershed. Support development of a coordinated database and clearinghouse for this information with other partners. Cost estimate: $40,000

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II.

•

Inventory and Map: Coordinate inventories and mapping of distribution and extent of key habitat types. Consolidate existing data and information. Identify inventory needs. Cost estimate: to be determined in 2004.

•

Invasive Exotic Species: Describe distribution and abundance of priority invasive non-native species. Consult the California Exotic Pest Plant Council and the Native Plant Society in developing this program. Prioritize containment and control of invasive non-native species, and implement management practices and monitor to evaluate effectiveness. Additional partners: Core group above and the Agricultural Commissioner’s office, Marin County, Marin Agricultural Land Trust, and State Coastal Conservancy. Cost estimate: to be determined 2004.

High priority, on-going activities to benefit habitat conservation and enhancement: •

Restore salmonid habitat and remove barriers to migration. Assess condition of salmonid and freshwater shrimp habitats. Specifically, identify limiting factors for salmonids and freshwater shrimp populations in Lagunitas Creek and analyze the limiting factors for salmonids in Walker Creek and other tributaries with historic runs. Lead: Marin Municipal Water District or Marin Resource Conservation District or Tomales Bay Watershed Council Partners: Point Reyes National Seashore, Salmon Protection and Watershed Network, Regional Water Quality Control Board, California Department of Fish and Game, State Coastal Conservancy, Marin County, Trout Unlimited, Tomales Bay Association, private landowners and others Schedule: 2 years for each study Cost estimate: $150,000 - $300,000 each

•

Support inventories and other studies of species of local interest and habitat assessments to identify habitat function, enhancement priorities and limiting factors. Partners: Tomales Bay Watershed Council and core group

•

Help landowners to protect and enhance riparian and wetland habitats. Promote and assist in coordination of all types of voluntary restoration efforts and projects. Partners: Tomales Bay Watershed Council and core group

•

Provide incentives and support for habitat protection and enhancement. Partners: The core group

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III.

•

Assure that regulated water releases by agencies and other entities with impoundments in the watershed are sufficient to sustain downstream cold water aquatic communities. Partners: The core group

•

Assess current water flow conditions and develop a plan to increase water flows if necessary to restore key habitats. Partners: The core group

Medium and long-term activities to benefit habitat conservation and enhancement: •

Ensure optimal streamflow to sustain native aquatic communities through water conservation and range management where feasible. Partners: The core group and private landowners

•

Ensure optimal streamflow patterns to sustain native aquatic communities by limiting the impacts of development (e.g. residential, commercial, public works and water) where feasible. Partners: The core group and local organizations (e.g. Marin Agricultural Land Trust, Inverness Public Utilities District, etc.)

•

Support funding for wetland protection and conservation easements on public and private lands. Partners: Marin Agricultural Land Trust, Natural Resources Conservation Service, Marin Resource Conservation District, California Department of Fish and Game, State Coastal Conservancy, Nature Conservancy, Audubon Canyon Ranch, U.S. National Park Service, State Parks, Trust for Public Lands, Marin County Open Space District, Environmental Action Committee of West Marin, landowners, and other local organizations

•

Identify policies that can be added to the Marin Countywide Plan that would include but not be limited to: 1. limiting the size of new residential structures by requiring that they fit current scale and size of existing structures in residential areas; 2. focusing development within current town boundaries; 3. preserving viewsheds; 4. protecting our natural resources; 5. discouraging fragmentation of agricultural lands; 6. supporting mariculture; and 7. supporting programs to keep large agricultural parcels intact. Lead: Tomales Bay Watershed Council via the Strategies Committee Partners: Marin County, village associations, local organizations

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•

Support policies that protect open space and agricultural land uses that are consistent with and contribute to watershed goals. Partners: Marin Agricultural Land Trust, Marin County, village associations, Environmental Action Committee of West Marin, Salmon Protection and Watershed Network, Tomales Bay Watershed Council

•

Support land uses that are consistent with and contribute to watershed goals. Partners: Marin County, village associations, Environmental Action Committee of West Marin, Council, Salmon Protection and Watershed Network, state and federal agencies

•

Survey conservation programs, priorities and funding needs of land conservation entities in the watershed. Develop recommendations regarding gaps in land conservation efforts and comprehensive funding needs in the watershed to ensure that important watershed habitats are being protected. Promote agency and NGO cooperation to increase efficiency. Lead: Tomales Bay Watershed Committee - Strategies Committee Partners: Marin Agricultural Land Trust, Audubon Canyon Ranch, Parks, PRBO, State and Federal agencies, California Department of Fish and Game/Wildlife Conservation Board, Marin County Open Space District

•

Protect unique habitats such as Tomales Dunes, coastal prairie and coastal scrub. Partners: Landowners, Environmental Action Committee of West Marin, Natural Resources Conservation Service, Audubon Canyon Ranch, National Park Service, Trust for Public Lands, State Coastal Conservancy, PRBO, Tomales Bay Association, Marin County

•

Protect and enhance native oak woodlands and other hardwood forests, and encourage restoration through outreach and support to private landowners. Partners: landowners, National Park Service, California State Parks, State Coastal Conservancy, Pacific Gas & Electric Co., Natural Resources Conservation Service, U.C. Cooperative Extension

•

Protect and promote restoration of proper functioning and hydrology of streams and floodplains. Partners: Point Reyes National Seashore, Marin County, California Coastal Commission, California Department of Fish and Game, NOAA Fisheries, landowners, CalTrans, Salmon Protection and Watershed Network, Coastal Conservancy, Audubon Canyon Ranch, Environmental Action Committee of West Marin, Marin Resource Conservation District, Natural Resources Conservation Service

•

Evaluate and optimize tidal circulation in leveed marshes. Partners: National Park Service, State Lands Commission, landowners, Gulf of the Farallones National Marine Sanctuary, Audubon Canyon Ranch, California State Parks, California Department of Fish and Game

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These activities will be successful if they achieve these results. Specific criteria will be developed on a project basis: 1. 2. 3. 4. 5. 6. 7. 8.

Practical understanding of existing habitats within the Tomales Bay watershed. Practical understanding of distribution and abundance of local species of interest. Practical understanding of distribution and abundance of invasive non-native species. Measurable terrestrial and aquatic habitat improvements on public and private lands, and within Tomales Bay and tributary streams. Demonstrable improving trends in habitat and species diversities in the Tomales Bay watershed. Demonstrable reduction in weed cover on range and grasslands in the watershed. Development of strategies to restore and protect habitat diversity in Tomales Bay and the watershed. Recommendations for prioritized habitat restoration and enhancement projects including potential funding sources.

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Action 4.0 Promote and support public outreach and education about Tomales Bay and its watershed. The Tomales Bay watershed comprises a diverse community of private and public landowners, villages and residents from the slopes of Mount Tamalpais to the town of Tomales and eastward to Chileno Valley. By working together with an expanded sense of community, we can protect the aquatic and terrestrial habitats that are essential to Tomales Bay as well as preserving the culture and heritage of the region. An aggressive public outreach and educational program directed at residents and visitors to the watershed will be essential to the reduction of the impacts of ever-intensifying patterns of usage. Action 4 calls for the involvement of all residents and users of the watershed to take an active role in the realization of the Plan’s goals. Local communities and the public in general must be given every opportunity to support the implementation of this Plan though participation in programs, and through media events that reach out to all interest groups. Purpose: • Encourage public awareness and participation in developing and implementing this watershed plan. • Increase public awareness of priority watershed issues. • Increase public awareness about efforts to reduce nonpoint source pollution. • Increase public awareness about opportunities to support and assist with endeavors to protect the bay and watershed. • Support watershed education in local schools. • Promote volunteer efforts. • Promote watershed stewardship. Lead: The Tomales Bay Watershed Council, via its Outreach Committee, will be the lead to undertake the high priority, short-term activities. I. High priority, short-term activities to increase public awareness and involvement in watershed stewardship. •

Seek public input on future amendments to the Tomales Bay Watershed Stewardship Plan. Partners: Tomales Bay Watershed Council member organizations and watershed partners

•

Enhance existing Council website and expand links to other local sites. Partners: Tomales Bay Watershed Council member organizations and watershed partners

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•

Submit periodic articles to local newspapers and give interviews to radio stations. Promote outreach efforts in Spanish. Partners: Tomales Bay Watershed Council member organizations and watershed partners

•

Facilitate information sharing about Tomales Bay and the surrounding watershed by sponsoring regular “State of the Bay” conferences, and create a repository for proceedings. Partners: U. C. Davis, Sea Grant Marine Advisor

•

Support outreach efforts to private landowners regarding incentive programs to reduce non-point source water pollution and habitat fragmentation. Partners: Marin Resource Conservation District, Marin County, Natural Resource Conservation Service, Salmon Protection and Watershed Network, Sierra Club, Gulf of the Farallones National Marine Sanctuary, State Coastal Conservancy

•

Promote education and outreach to encourage responsible human recreational activities which can disturb wildlife, and dissemination of information about existing policies to protect marine mammals, shorebirds, sensitive plant communities, etc. Partners: Tomales Bay Watershed Council member organizations and watershed partners

•

Develop an educational flyer/brochure about watershed conservation, collaborative efforts by local stakeholders, and restoration efforts to place at locations visible to the community and visitors, including: bed & breakfasts, state and national parks, inns and other commercial establishments including kayaking companies, Lawson’s Landing, Miller Park, Marshall Store, oyster companies, and restaurants.

•

Support project-based learning efforts such as those organized by STRAW, West Marin School, SPAWN, Adopt-A-Watershed, etc. Partners: Tomales Bay Watershed Council member organizations and watershed partners

•

Develop and disseminate an updated bibliography of scientific literature on Tomales Bay. Partners: Sea Grant Marine Advisor- UC Davis, U.C.Cooperative Extension, Tomales Bay Association

•

Continue an annual newsletter to be sent out to all residents in the watershed, and consider combining with local organizations’ newsletters to increase visibility and readership. Post Council newsletter electronically on the Council website, and if possible on other websites.

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•

Develop a list of volunteer opportunities in the watershed- avenues for active engagement. Include this material in our outreach materials and website. Query local groups and agencies on their volunteer needs and programs.

II. Medium and long-term activities to increase public awareness about watershed stewardship: •

Promote education and outreach to encourage water conservation and the importance of installing common household low-water usage appliances (e.g. low flow toilets), and use of appropriate landscaping practices (e.g. planting native, drought tolerant plants). Partners: Marin Municipal and North Marin Water Districts, Marin County

•

Promote watershed education at schools and summer camps in West Marin. Partners: Tomales Bay Watershed Council, Point Reyes National Seashore Association, Students and Teachers Restoring A Watershed (STRAW), Salmon Protection and Watershed Network, Shoreline Unified School District, Lagunitas and Nicasio School Districts, school staff and science teachers, students, Gallery Route 1, State Coastal Conservancy

•

Support development and dissemination of watershed-based curricula to local schools. Promote and enhance watershed education efforts at local schools. Partners: Tomales Bay Watershed Council, Point Reyes National Seashore Association, Tomales Bay State Park, Salmon Protection and Watershed Network, Gulf of the Farallones National Marine Sanctuary, STRAW, Shoreline Unified School District, Lagunitas and Nicasio School Districts, Gallery Route 1, Tomales Bay Association, State Coastal Conservancy

•

Promote watershed educational outreach opportunities including hikes, tours, seminars, etc. Participate in and support existing efforts. Provide information on on-going volunteer opportunities with partners in the watershed (i.e. SPAWN, PRBO, MALT, Marin RCD, PRNS, Audubon Canyon Ranch, etc.) Partners: Tomales Bay Watershed Council, Outreach Committee

•

Promote stewardship through annual land steward award. Partners: Environmental Action Committee of West Marin, Tomales Bay Association

•

Hold tours of demonstration projects. Partners: Marin Resource Conservation District, Marin Agricultural Land Trust, Salmon Protection and Watershed Network, Environmental Action Committee of West Marin, Marin County

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•

Develop stewardship education packets. Partners: Marin Resource Conservation District, Conservation Service, Tomales Bay Watershed Council

•

Develop a “coffee table” book featuring the Tomales Bay watershed. Partners: Tomales Bay Watershed Council - Outreach Committee, Point Reyes National Seashore, others

Natural

Resource

Cost estimate: $20,000 estimated annual budget for Council outreach activities These activities will be successful if they achieve these results. Specific criteria will be developed on a project basis: 1. Creation and dissemination of watershed education materials to communities in West Marin using different media on a regular basis during 2002-2004. 2. Development and maintenance of a website to facilitate education and information sharing about Tomales Bay and its watershed during 2002-2004. 3. Sustained community participating and interest in the Council’s watershed planning activities.

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IV. ACTION PLAN IMPLEMENTATION “Every Day I feel lucky to live and work here. It is only natural to want to protect Tomales Bay, its hills, streams, forests, and wildlifeand also the vitality of its communities, its small villages, and its farmlands.” -- Ellen Straus, Dairy Rancher

A. Partnerships and Collaboration There are many different actions needed for a healthy watershed. These actions include community outreach and education about watershed stewardship, habitat restoration, political advocacy, promotion of incentive programs to support the voluntary efforts of private landowners, and regulatory enforcement. By working together through partnerships, local communities, agencies and organizations can protect and improve the health of Tomales Bay and its watershed. Through monitoring, we can increase our effectiveness and engage in adaptive management as we progress towards our goals. The Council will support implementation of this Plan, taking on specific programs and projects that are beyond the mission or capacity of individual organizations/agencies or established partnerships. The collective resources of the members of the Council are necessary for successful and timely planning, assessment and implementation of watershed restoration activities. Working together within the Council will help ensure the most protective and cost-effective watershed enhancement efforts, and the extensive work ahead requires the support of residents and the communities in West Marin. The Council will also continue to provide a forum where programs and projects are discussed and evaluated. The Council provides a venue for the expression of concerns and ideas for the collective management of this watershed and supports any effort to achieve the Plan goals. To facilitate improved collaboration and coordination between agencies, and to promote partnerships between with other stakeholders in the watershed in the future, the Council will: • Work with agencies to facilitate needed communication and information dissemination between and within agencies. • Host an annual or semi-annual meeting of agencies to evaluate progress for priority activities identified by the Council, and identify needs and gaps. • Provide feedback/comment on planning efforts of local, state and federal agency partners as requested. • Invite relevant agencies to present at monthly Council meetings and host community meetings as necessary.

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B. Future Steps for the Tomales Bay Watershed Council The Council is committed to continuing its activities during the next 5 years as it develops needed programs and recommendations to guide restoration, assessment and monitoring activities in the watershed. To date the Council’s organizational structure has supported the development of this Plan, and during the next year the existing Council will evaluate its own structure to identify how it can best facilitate implementation of the recommendations within this Plan in the future.

1.0 Council priorities In the future, the Council will provide necessary support to partners in the watershed to ensure meaningful and effective progress towards the Council’s vision for the future. In addition, the following table summarizes the activities for which the Council is the lead, and these activities will be the Council’s priorities during the next three years. The Tomales Bay watershed is a dynamic system. As issues evolve, as social, political and economic realities change, and as available funding for watershed planning and stewardship waxes and wanes, the Council will reconsider its priorities and modify its direction and focus as needed. Tomales Bay Watershed Council priorities for the next three years are captured in Table 1.

2.0 Administrative Activities The Council will consider its future role in the Tomales Bay watershed and existing administrative needs during the next year, and will develop a strategic work plan to this end. More specifically, we wish to establish a Council that can: • Encourage comprehensive resource planning and facilitate interagency coordination and cooperation to achieve Plan goals. • Continually update the Tomales Bay Watershed Stewardship Plan with new assessment data, monitoring and restoration project reports, and recommendations for future action. • Monitor implementation of this Plan. • Identify opportunities to influence and support local, state and federal policies that help to achieve the Plan’s goals. • Provide a forum for stakeholders, the public, regulatory agencies and research groups to interact and facilitate implementation of TMDL plans and other programs affecting the health of the bay and watershed. • Support activities of local agencies and organizations to implement projects and programs to reduce the impacts human activities on the watershed and bay. • Encourage interaction between stakeholders • Facilitate volunteer programs to assist with research, restoration and monitoring projects. • Promote understanding of Tomales Bay and its watershed through outreach and education. Tomales Bay Watershed Stewardship Plan: A Framework for Action 77

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Table 1. Tomales Bay Watershed Council Priorities 2003-2005

Activity 1. Undertake Action 1, the development of a water quality monitoring plan for Tomales Bay and tributary streams. 2. Develop a salmonid assessment and restoration priorities report for the Tomales Bay watershed, including criteria for salmonid restoration project selection. 3. Work with lead agencies on 3-5 high priority activities in the Action Plan, and facilitate needed action by these parties. 4. Develop a Strategic Work Plan for the Council and revisit the Coordinated Resource Management Planning (CRMP) process and as an option for facilitating future programs/projects. 5. Advise on the development and implementation of the Lagunitas Creek Watershed Improvement Program in collaboration with the Marin RCD. 6. Finalize the Draft Habitats and Species Appendices, promote public review and amend them to this Plan. Consider Marin County’s Survey of Recreational Impacts on Tomales Bay for amendment to this Plan. 7. Develop and distribute a summary of current activities to improve and protect water quality and habitats in the Tomales Bay watershed, including: project/program description and location, lead(s), funding, timeline, etc. Update this list annually. 8. Support implementation of the Pathogen TMDL for Tomales Bay by disseminating information to watershed stakeholders and hosting community meetings. 9. Undertake education and outreach activities specified in Action 4. 10. Host a State-of-the-Bay Conference

Timeline Begin Sept. 2003, Plan due Dec. 2004* Due December 2003*

Due December 2003*

Due January 2004*

On-going 2003-2006*

Due July 2004

Due July 2004

On-going 2003-2005 On-going 2003-2005* 2005

*Note: The above activities with an asterisk by the due dates are partially or entirely funded by grant awards received from California Department of Fish and Game, State Water Resources Control Board (Prop. 13 Program), and Marin Community Foundation. Project due dates are established in each of the respective contracts.

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I. High priority, short-term activities for the Council to undertake in development of a strategic plan. See reference year following each step.

II.

•

Define capacity and structural needs of the Council for facilitation of Plan implementation. Determine future organizational structure, membership, staffing needs, funding, operating rules and procedures, etc. needed to sustain the Council for 5 years. Identify the issues that must be addressed for the Council to remain a vital stewardship organization for Tomales Bay planning and protection activities. (2003) Lead: Tomales Bay Watershed Council and committees Partners: federal/state/local agencies, local non-governmental organizations, community members

•

Define roles and responsibilities of Council members and other stakeholders related to Plan implementation. Consider spectrum of activities that include technical advising, financial contributions, organizational support, political networking, etc. (2003) Lead: Tomales Bay Watershed Council and committees Partners: federal/state/local agencies, local organizations, community members

•

Develop a budget and funding strategy to support the Council and Plan implementation considering high priority short-term actions proposed in this Watershed Stewardship Plan. Consider internal capacity to acquire funding for basic administrative and organizational needs from member agencies and organizations; foundations for long-term and programmatic support, and grant opportunities for projects. (2003) Lead: Tomales Bay Watershed Council - Executive and Funding Committees and fund-raising experts

•

Define a regular meeting schedule that members and participants support to facilitate collaboration between stakeholders, information sharing and opportunities for public involvement in the planning process. Authorize and monitor action-oriented committees to carry out the Action Plan between these meetings. (2003) Lead: Tomales Bay Watershed Council - Executive Committee

Medium priority, medium-term activities •

Amend this Watershed Stewardship Plan. Expand existing appendices with data analysis, assessment and project information, etc. Revisit and revise as needed priority recommendations. Include a process to adapt management recommendations based on the results of monitoring activities (2003-2005). Lead: Tomales Bay Watershed Council and committees

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•

Consider regional issues and other models for watershed planning. Invite planning experts to address Council on regional issues, projected growth and development, and related impacts. Include national and state parks, Association of Bay Area Governments, Marin County, local academic institutions, the State Coastal Conservancy, California Coastal Commission. Review the effectiveness of watershed planning efforts elsewhere and invite experts to address the Council regarding these programs. Involve the State Coastal Conservancy, Morro Bay and/or Tillamook National Estuary Projects, U.S. EPA, Monterey Bay Water Quality Protection Program, and others as determined. (2003-2004) Lead: Tomales Bay Watershed Council - Strategies Committee

•

Identify and review existing laws, zoning, policies and regulations as they relate to Plan goals to assure their appropriateness and effectiveness. Identify gaps or needs within the existing framework. Develop recommendations for revision on an as needed basis. Lead: Tomales Bay Watershed Council - Strategies Committee

These activities will be successful if they achieve these results. Specific criteria will be developed on a project basis: 1. Significant enhancement of the Council’s structural, programmatic and financial capacities. 2. Annual progress towards implementation of the recommendations in the Watershed Stewardship Plan. 3. Sustained collaboration and networking among watershed stakeholders.

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V. APPENDICES A. Water Quality Status and Trends Report B. Erosion & Sedimentation in the Tomales Bay Watershed C. Glossary of Common Ecological and Watershed Related Terms D. Summary Responses to Public Comments

Additional information: Appendices describing habitats and species found within the Tomales Bay watershed are being developed by the Council and are forthcoming. These reports will be amended to this plan after public review and adoption by the Council.

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Appendix A. Water Quality Status and Trends Report 1.0 Introduction and objectives The objective of this water quality narrative is to review existing literature from Tomales Bay and tributaries in order to understand the status and trends of contaminants found by these studies. The emphasis is on the water quality parameters that have exceeded the Regional Water Quality Control Board’s (RWQCB) Basin Plan standards, the Department of Health Services (DHS) and the National Shellfish Sanitation Program (NSSP), and have as a result caused the listing of Tomales Bay as impaired under the Clean Water Act. It is important not to lose sight of the fact that the bay and adjacent watershed makes up an interrelated ecosystem and that these factors of concern are only part of a complex system. Thus, other aspects of the Tomales Bay ecosystem must also be studied, evaluated and perhaps monitored to protect the beneficial uses of the estuary. Most of the report relies on existing data analysis and conclusions drawn by the responsible authors. Data was extracted from a number of studies that used bivalves to bioconcentrate contaminants from Tomales Bay. The status and trends, when possible, were presented for each of four contaminants: pathogens; nutrients; mercury contamination; and sediment inputs into tributaries and the bay. The outcome of this review is the listing of data gaps and recommendation on studies that could obtain additional data needed to further understand the bay and watershed processes. Recommendations were proposed for issues that need to be addressed by organizations involved with Tomales Bay watershed management. The objectives of the narrative are: 1) to review relevant studies of the bay dating back to 1960; 2) to summarize existing conditions based upon historical and current monitoring data; 3) to identify water quality problems and pollutants of concern based on the literature review and discussions with leaders of ongoing programs in the bay; and 4) to develop a discussion of gaps in existing data and an overview of the necessary studies and information needed to fill the data gaps. The narrative addresses primarily water quality issues. References to impacts on biological communities and/or species are presented only if well documented and important to understanding the stated objectives. Since the emphasis is on water quality the majority of the data reviewed will relate to materials in suspension in the water column or found in bivalve tissue. Thus, stream bedload transport, erosion patterns, and sediment transport from tributaries or within the bay are not evaluated except as they relate to the mercury contamination problem. No evaluation of current or past best management practices, or restoration actions within the watershed is presented nor is ground water contamination addressed in this narrative. There is no attempt to evaluate the quality of the data, status of the QA/QC protocol for data analysis and presentation, or any attempt to evaluate the validity of the conclusions of the information reviewed. Because of the lack of data analysis only the most apparent data gaps are presented.

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2.0 Water Quality 2.1 Bacterial contamination and other water borne pathogens A large effort has been sustained during the last 20 years to investigate the cause, frequency and sources of bacteria contamination that effect the harvesting of shellfish in Tomales Bay. Bacteria are a potential threat and common indicator of water borne pathogens that can effect human health and other living organisms, and may indicate the presence of viruses and parasites, in addition to other types of water contamination that are more difficult to assess. These bacteria focused studies have dealt primarily with total and fecal coliform potentially coming from a number of possible sources including dairies and ranches, from substandard or failing sewage systems, and from natural populations of wildlife that live in or visit the bay and surrounding watershed. Under section 303(d) of the Clean Water Act Tomales Bay has been listed as impaired due to pathogens (Taberski, 2000) for the following reasons: 1. Tomales Bay is closed to shellfish harvesting for an estimated 90 days a year, therefore it is assumed that the standards set by the RWQCB (basin plan), DHS and U.S. Food and Drug Administration (FDA) are exceeded 90 days per year. 2. Under the state’s Shellfish Protection Act (California Water Code), Tomales Bay is considered “threatened” due to the shellfish harvesting closures listed above. 3. DHS prohibits shellfish harvesting during periods of rainfall based upon the results of bacteriological studies. In 1997, closure rules for shellfish harvesting were made more stringent. Thus, the beneficial use of shellfish harvesting is not protected during the wet weather season. 4. During periods without rainfall and when bacteriological objectives were met there was a major human illness outbreak of a virus of human origin from consumption of oysters. This fact shows that the beneficial uses of Tomales Bay were not protected even when water quality objectives were met. On October 10, 1993, legislation was passed by the California legislature that enacted the Shellfish Protection Act of 1993. This bill requires the RWQCB to form a technical advisory committee for any commercial shellfish growing area that is determined to be threatened. One of the criteria for the formation of the committee was that if a shellfish harvesting area is closed for more than thirty days in each of three consecutive years a committee must be organized. Tomales Bay met this requirement and the Tomales Bay Shellfish Advisory Committee (TBSTAC) was formed on February 15, 1994 (TBSTAC, 2001). 2.1.1 Literature overview As early as 1967 when the Pacific Marine Station and the North Marin Water District (NMWD) undertook water quality studies it was found that Tomales Bay had fecal coliform levels that were high during the winter runoff periods (Smith et al., 1971). Even under the shellfish harvesting standards in effect during the study period, the requirements were only met between July and September of each year (Smith et al., 1971). Tomales Bay Watershed Stewardship Plan: A Framework for Action 83

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The California Department of Health Services conducted a detailed water quality survey of Tomales Bay and tributary streams during wet weather conditions to evaluate the bacteriological quality of the shellfish grown in the bay (Sharpe, 1974). Dry conditions in the watershed during the study period resulted in runoff that was not great enough to result in significant degradation of the bay surface water quality. The study was started after a threeday rainfall of 1.98 inches with only some shoreline sampling stations affected by runoff. Water quality stations were located at 17 sampling stations, 19 shoreline stations and 49 stream stations. The sampling effort continued for 12 days in December. Shellfish tissue samples were also analyzed for coliforms and heavy metals. Samples from the bay did not exceed the median standard of 14 MPN/100 mL required for shellfish harvesting, although a few stations did exceed the required 90th percentile of 43 NPM/100 mL. Stations along the shoreline had elevated levels of total and fecal coliform. Sharp (Sharpe, 1974) considered the tributary streams to be the major pathway of coliform entering the bay and he attributed the source of the coliform bacteria to waste material from dairy cattle in the watershed. Other sources of potential contamination were investigated including raw sewage from the town of Tomales (this study was conducted before the town of Tomales completed construction of a sewage treatment plant), faulty septic systems, boats and boating facilities, the park systems, and ducks and other birds. None of these possible sources of contamination were considered to be major factors in the bacteria associated degradation of the bay waters. Only 5 of the 22 (22.7%) shellfish samples analyzed met the recommend standard for harvesting. The results of this study indicated the need for all shellfish growing areas within Tomales Bay to be “Conditionally Approved.” A two-year study was conducted during the winters of 1976-77 and 1977-78 by the San Francisco RWQCB (Jarvis et al., 1978) to evaluate the effectiveness of the RWQCB’s requirements for dairy waste practices. Twenty stream stations and six shoreline stations were established for the study. Not all the stations were sampled both years and during each survey period. An analysis of total and fecal coliforms, ammonia and total organic carbon were completed for the samples collected. The results indicated that the coliform quality of streams that are tributaries to Tomales Bay seemed to have improved between 1974, before the implementation of the “Minimum Guidelines for Protection of Water Quality from Animal Wastes” and the period after the guidelines were established and covered by the study period (1976-77/1977-78) (Jarvis et al., 1978). Creeks that had dairies in their drainage areas had higher coliform levels than creeks without dairies. Some areas of the watershed that had no dairies also had substantial levels of coliform during rainfall runoff in 1977-78. The authors attribute that to animals on pasturage, wild animals, and naturally occurring coliform from the soil and vegetation. Ammonia concentrations did not exceed water quality standards, except for two stations (affected by dairy wastes) during 1976-77. Shellfish harvesting was affected when coliform levels exceeded the allowable limit and resulted in the closure of one aquaculture facility for two months. The authors also observed that: “it is unlikely that Tomales Bay will ever meet coliform objectives for shellfish harvesting during periods of substantial rainfall runoff even if all the dairies met the Minimum Guidelines”. Tomales Bay Watershed Stewardship Plan: A Framework for Action 84

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An FDA sanitary survey was conducted from February 24 through March 12, 1980. The primary objectives of the study were to collect water quality data during and following a period of rainfall from which the following could be determined: 1) how much rainfall requires a closure to shellfishing and in what period of time; 2) how long the bay takes to recover from such a contamination event; and 3) what portions of the bay are most affected (Musselman, 1980). In addition, the study was to determine what the sources of pollutions were and to assess the hazard level, and to compare data from DHSs routine monitoring program with the results of this study. Forty-five stations were established in the bay and on tributaries near where they empty into the bay. A total of 393 samples were collected and analyzed for total and fecal coliform and fecal streptococci. Shellfish tissue was collected at two stations in the bay and tested for total and fecal coliform. The results indicated that intermittent periods of rainfall caused large variations in the water flowing in the streams during the survey. These flow changes were accompanied by wide variations in the bacterial levels with total coliform ranging from 230 NPM/100 ml in Bear Valley Creek after a few days of dry weather to 97,000 NPM/100 ml in Tomasini Creek during a heavy runoff event. The portions of the bay most seriously affected by bacteria contamination resulting from rainfall and runoff are the inner bay, Millerton Point to the south; and the east side of the outer bay, inside the mouth including the Walker Creek Delta. Seven out of eight shellfish tissue samples exceeded market standards. Bacterial ratio analysis in stream and bay waters indicated that a mixture of rural and livestock non-point pollution was the most likely source of high bacterial counts in the bay. A small study was conducted by DHS in 1982 with 21 boat stations in Tomales Bay and 19 stations in tributary streams that were sampled during a rainstorm from March 1 through March 5 (Hultquist, 1982). Samples were analyzed for total and fecal coliform and fecal streptococcus. The results of this unpublished report follows the established pattern in earlier studies of high coliform levels during the storm runoff and then rapidly declining concentrations during the following drying period. DHS conducted studies during 1994-95 to evaluate indicator species, test sampling methods and laboratory analyses and to finalize site selection of watershed sampling stations for a later investigation in 1995-96. During this pilot study a total of 352 samples were collected from 12 stations in the Tomales Bay and from 35 watershed locations. Samples were collected from this array of stations nine separate times covering periods when the shellfish harvesting was both open and closed. These samples were analyzed for total and fecal coliform, Enterococci, Bacteroides species, Clostridium perfringens and Methylene BlueActive Substances (MBAS), which are common surfactants in detergent. These indicator species were selected by TBSTAC as a preliminary effort to evaluate the use of more selective test procedures (TBSTAC, 2001). Shellfish tissue was sampled from 26 organisms and analyzed for total and fecal coliform (DHS, 1996). Results of this investigation were similar to earlier studies and verified that during periods of rain the tributaries entering Tomales Bay contributed bacteria to the bay system. Two seasonal patterns of fecal coliform concentrations were noted: 1) sites that showed declining fecal coliform densities throughout the winter, that suggested a nonrenewable source as the runoff declined and, 2) sites that Tomales Bay Watershed Stewardship Plan: A Framework for Action 85

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exhibited high fecal coliform concentrations throughout the winter season, suggesting a renewable source (Taberski, 2000). The 1995-96 sampling program was designed by Tomales Bay Shellfish Technical Advisory Committee (TBSTAC) and conducted by DHS (Taberski, 2000; TBSTAC, 2001). This study was a joint effort of DHS, RWQCB and funded by SWRCB. Samples were analyzed for total and fecal coliform, enterocuccus and Escherichia coli. In addition to the parameters measured in the earlier study, several sites were analyzed for coliphage and the anaerobic bacterium Bacteriodes vulgatus, which is an indicator that is thought to be more specific for human fecal sources than the standard indicator organisms (Taberski, 2000). A limited number of samples were analyzed for the pathogenic bacteria Salmonella typhirium and E. coli:0157. The study was conducted in the winter of 1995-96 and samples were obtained from 40 stations located in the bay and watershed. The collecting periods covered two dry phases and four rainfall events. Sample collection during wet events extended past the period when the bay would be opened for shellfish harvesting (day 10 after the first rainfall). The results from this intensive study were used, in part, to establish numeric targets for the Total Maximum Daily Load (TMDL) process (Taberski, 2000; TBSTAC, 2001). These results are summarized below: 1. Bacterial densities usually exceeded the standards within the first one or two days of each rainfall event and then decreased to within requirements by the end of sampling. This fact follows the finding of all the earlier studies reviewed for this report. 2. High bacterial levels were consistently recorded for the Walker/Keyes/Chileno watershed and along the eastern shoreline of the watershed. Slightly lower levels of fecal coliform were detected throughout the Lagunitas/Olema subwatershed with Lagunitas Creek contributing the largest share of fecal coliform to the bay, followed by Olema Creek. Bear Valley drainage contributed the lowest amount from this sub-watershed. The fecal coliform concentrations along the western shoreline were 10-100 times lower than in the other watersheds. 3. Samples collected in the bay were also affected and were above standards within the first two days following significant rainfall. The fecal coliform levels remained above requirements for three days after the rainfall event and did not always return to levels below the standard for shellfish growing regions after bay waters were open for harvesting (day 10). A station (34) directly influenced by outflow from the Walker Creek drainage around Preston Point had the highest levels of fecal coliform. Stations sampled in mid-bay had fecal coliform levels that were usually lower than those stations located in the outer bay or inner bay although all were elevated. 4. Samples taken from oyster tissue collected at outer bay stations reached extremely high levels following significant rainfall and followed the pattern seen in the water column analysis where levels did not return to the NSSP market standards after the bay was opened for harvesting. The data also indicated a pattern of increasing fecal coliform Tomales Bay Watershed Stewardship Plan: A Framework for Action 86

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levels throughout the winter period. At some of the outer bay stations samples were taken from oysters growing in floating bags (top culture) and bottom-cultured bags. Those oysters raised under surface conditions had significantly higher levels of fecal coliform (above NSSP standards) during the first dry period sampling, which might be related to local contamination sources possibly from birds (Taberski, 2000). What portion of the increasing fecal coliform levels that occur throughout the winter period in the bay come from the watershed and/or local sources near the shellfish growing areas was not clear in the report. 5. The four commonly used indicator organisms were monitored during this study to evaluate if any single indicator was more source-specific than others. Levels of E. coli tended to drop more slowly than the other indicators, and was often the only indicator exceeding the acceptable standard by day 3 of the monitored rainfall events. Based on these results, enterococcus was determined to be the most sensitive and fecal coliform was the least sensitive indicator organism relative to their respective water quality objectives. A joint study in 2000-2001 was undertaken by the RWQCB and National Park Service (NPS) to investigate water quality in the Lagunitas Creek and Olema Creek sub-watersheds (Ketcham, 2001). For the Tomales Bay Pathogen Study, 25 stations were sampled during the rainfall events. Other water quality parameters were also collected and included ammonia, DO, pH, conductivity, TSS and temperature. At these sites one or two samples were collected in a given day. Two time series stations were designated (Olema Creek at Bear Valley Road Bridge and Lagunitas Creek at the USGS gauging station). At these stations the sampling was much more intense and was intended to document the response of E. coli levels in relation to the monitored hydrograph. Collections were spread across the rising and falling limb of the hydrograph to determine pathogen delivery response in relation to the stream flow. Thus, samples were collected every one to four hours for the duration of the study (up to four days). Analysis of the data demonstrated that Olema Creek watershed had one of the lowest fecal coliform and E. coli loadings to the bay. Loading results from Lagunitas Creek indicated that it was a larger contributor of fecal coliform and E. coli to the bay than Olema Creek. Even though bacterial concentrations were always lower in Lagunitas Creek than Olema Creek, the stream flow effected the calculations of loading so that Lagunitas was higher than Olema. The report speculated that agricultural sources are the major contributors of fecal coliform and E. coli to the bay, . . However, high levels of these pollutant parameters observed in San Geronimo Creek and from Point Reyes Station storm drains indicates that developed areas cannot be discounted as a source (Ketcham, 2001). Toxic ammonia was not a problem except for one sample taken from pasture runoff in the Giacomini tributary to Olema Creek. 2.1.2 Agricultural runoff and sub-watershed contributions of water borne pathogens All of the bacterial studies reviewed in this document have indicated that animal based agricultural runoff plays a major role in the high levels of fecal coliform recorded in Tomales Bay Watershed Stewardship Plan: A Framework for Action 87

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tributaries from the watershed and in Tomales Bay during the rainy season. Throughout the watershed, grasslands and pastures are used for cattle and other livestock grazing on public and private lands. Estimates have been made on a pounds per day of total waste (fecal and urine) production by a typical animal. Based on a survey in 1990, (Bennett, 1992) it was estimated there were approximately 10,970 head of dairy animals, 1,320 head of beef, and 1000 sheep that utilized the Tomales Bay watershed (includes Chileno Creek, Keyes Creek, Walker Creek, Marshall to Point Reyes Stations and the Lagunitas/Nicasio Reservoir). Using these figures, the total count of 13,290 animals produce 1,073,775 lbs/day of manure (corrected figures from Taberski, 2000). These calculations need to be revised to reflect current livestock animal populations and management practices. In order to address this problem and to assist the agricultural community in maintaining a viable enterprise the Tomales Bay Agriculture Group (TBAG) was formed in 1999. To assist with these water quality efforts, the University of California Tomales Bay Water Quality Project has implemented a “systems approach” to study animal agricultural facilities (Lewis et al., 2001). This systems approach was designed to evaluate possible links between animal agriculture and fecal coliform, nutrients, and sediment loading to the bay. Facility evaluations were conducted in a four-step process; which included a facility tour and sampling site selection, first storm-event sampling, second storm-event sampling and on site discussion of the preliminary results with participating members of TBAG. With ten participating producers and a limited number of storms during the two-year period of the study 19 first-storm event samplings and 6 second-storm events were studied for a total of 25 sampling events. Sampling locations during storm events for facility scale investigations were selected to compare management practices with respect to water quality for the investigated parameters. This study has grouped loading units into subcategories that included; waste management systems (WMS) such as retention ponds and flush systems, pasture, lots used during the summer, manure stockpiles, drains not in contact with animals facilities, runoff from impervious surfaces and roof runoff before it entered subsurface drains. In addition to the facility loading unit evaluation, tributary scale sampling and analysis was conducted to establish a water quality baseline. Control watersheds were selected which did not have dairy facilities or development and had limited rangeland usage by cattle or wildlife. Tributaries that represent upstream conditions just before a stream passes through a facility unit that was to be evaluated were selected. Stations were located downstream on the tributary that passed through the facilities. Bay sediment samples were also collected during low tide periods near leased shellfish growing tidal flats. Six transects with random samples were taken before rains (September 2000), during rains (March 2001) and after winter rains (late May 2001). In addition to these samples sediment was also collected from tributary streams and Tomales Bay shoreline. This study showed that mean fecal coliform instantaneous load and storm load for control and upstream were not significantly different. This is important given that upstream units were managed for grazing and received spread and irrigated manure (Lewis et al., 2001). Mean fecal coliform concentration, instantaneous load and storm load were significantly

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greater downstream from facilities than the control. Both fecal coliform concentrations and storm load were significantly greater downstream than upstream of facilities. Data from the sediment analysis shows a significantly greater mean fecal coliform concentration in tidal flat sediments during the winter than during pre-or post- winter periods. Specific loading units, in order of concern, for fecal coliform include: stockpiles, lots, storm drains, and facility runoff (Lewis et al., 2001). Potential fecal coliform loading in runoff from stockpile areas and lots is two and in some cases three orders of magnitude greater than loading from other units (Lewis et al., 2001). In comparison, fecal coliform loading from pastures is not significantly different from upstream or runoff loading units. Focusing efforts to reduce or store this volume of runoff, or lowering the concentration of fecal coliform from lots and stockpiles, would contribute to a reduction of the overall potential loading within agricultural tributaries. Staff from the Department of Fish and Game (CDFG) has been involved since the early 1970s with the dairy industry to assist in the promulgation of guidelines to reduce the waste material that enters streams near confined animal operations (Rugg, 1992). Most of the attention has been focused on bacterial contamination moving down tributaries and entering Tomales Bay and effecting the harvesting of shellfish during wet weather periods. However, in response to dairy waste pond failures, CDFG has found that soluble organics, principally ammonia, are of even greater importance than the bacterial levels because ammonia is extremely toxic to aquatic organisms. Based upon this information a program was started in 1991 and continued through 2001 (Rugg, 2000; Rugg, 2002). The program consists of 20 stations in the Tomales Bay (20 more stations were located in Sonoma County, outside the area of interest) that were monitored from the onset of sustained flow in most watersheds, through the middle of June, or whenever flows ceased. At each sampling station a number of parameters were measured including dissolved oxygen (DO), total ammonia, un-ionized ammonia and conductivity. The stations were located along the south and eastern shoreline of Tomales Bay at bridges or culverts under Hwy 1, wherever flow could be sampled. Data was evaluated for the periods from 1998 through 2001 in this agricultural runoff investigation. Results from the 1998-99 period indicated that out of 329 measurements the water quality parameters in the watershed were very good, with only three exceptions being recorded (DO levels and un-ionized ammonia). D.O. was consistently at or near saturation; total ammonia was low, with a notable exception of one elevated ammonia reading. The toxic form of ammonia was low and conductivity showed some slight improvement from earlier studies (Rugg, 2000). The nearly normal winter did not create any serious water quality problems in most streams within the study area. Results for the periods from 1999-2000 indicated that the streams in the watershed were in very good condition. Dissolved oxygen was consistently at or near saturation, total ammonia was low and conductivity was extremely low. It should be noted that the conductivity data might be somewhat ambiguous as some sampling locations within the watershed are periodically subject to tidal inundation (Rugg, 2002). There were no recorded samples that exceeded the ammonia criteria for the year, and only two for dissolved oxygen.

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2.1.3 Non-agricultural sources of water borne pathogens There are eleven small towns within the watershed. All of the towns are served by onsite sewage disposal systems except for the town of Tomales, which is served by a centralized wastewater treatment plant (TBSTAC, 2001). There are eight small sewage treatment systems within the watershed, and one facility that accepts septage waste. Four of the facilities discharge effluent onto the land, and five facilities utilize leach fields for dispersing effluent in the ground. Since most of these facilities are located near streams there is always the chance of a plant accident that could cause an effluent discharge to a local tributary and possibly into Tomales Bay. The only preventive steps that can be taken in case of a spill is to have response plans in place to reduce the effect of the spill and to notify such activities as shellfish harvesting of the potential danger. During the review of files and site inspections DHS noticed considerable variability in waste discharge requirements, operator certifications, and site regulations for various permitted waste facilities (TBSTAC, 2001). There are many non-point sources of pollution in the Tomales Bay watershed. The potential for failing septic systems in areas around the bay has been of concern to public officials for a number of years particularly in regions where growth would cause expansion of septic system usage. As far back as 1978 there was concern that nitrate pollution could occur from Inverness housing developments using septic systems and located near Brook Ness, Alder Creek and other locations (Clark et al., 1978). Leakage into the creek drainage areas could cause nutrients to enter Tomales Bay. The unincorporated areas around the bay are served entirely by various types of onsite sewage disposal systems including septic tank and leachfield systems, holding tanks, and sewage pits (TBSTAC, 2001). These systems are most likely to fail during times of heavy rainfall with resulting high groundwater. Stormwater runoff from residential and commercially developed areas represents another potential source of pollutants to both tributaries and the bay. Storm drains in small villages in the watershed can act as effective conduits for a spectrum of contaminants including pathogens, motor oil, detergents and herbicides/pesticides. The hydrology of our communities beyond the storm drains is such that a vast array of human activities -- from construction and maintenance of roads, to building and industrial sites, to horse paddocks in backyards -- all pose significant impacts to the water quality of the watershed. Federal, state, and county agencies are all mandated to address and reduce pollution from these sources. In 1995 the Marin County Stormwater Pollution Prevention Program (MCSTOPPP) was created to link federal and state mandated programs with community efforts to improve water quality, preserve and enhance riparian and wetland habitats. Within the RWQCB’s stormwater conveyance program, and in conjunction with the TMDL program, MCSTOPPP will begin in March of 2003 to develop, implement, and enforce a stormwater management plan (SWMP) for the Tomales Bay watershed that will include monitoring as well as public outreach and education. Additional sources of bacteria in Tomales Bay and its watershed include domestic animals, excretions from wildlife that include waterfowl and marine mammals as well as terrestrial animals, that enter either directly to bay waters or through tributaries. The amount of Tomales Bay Watershed Stewardship Plan: A Framework for Action 90

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“background” loading that comes from these wild populations is not known. However, large populations of wintering water birds (e.g., 11,800 in winter of 1998-1999, not including gulls) occur in the vicinity of shellfish growing areas (Kelly and Etienne, 1999). In addition, some 7,400 were observed roosting on the Walker Creek Delta encompassing an area of about 2 hectares of tidal flat (Kelly et al., 1996). Of the marine mammals that can be found in Tomales Bay, harbor seals are the most abundant and have haul-out sites around Hog Island and in the Lawson’s flat area near the bay mouth. Surveys by the National Park Service estimate that populations range from 400 to 650 year round, of which 100-200 individual are considered to be resident in Tomales Bay. The haul-out areas are not directly in any of the commercial shellfish growing areas (TBSTAC, 2001). Floating structures that support shellfish culture bags are attractive roosts to both birds and marine mammals. Recreational and commercial boats are found distributed throughout the bay, and are a potential source of human waste and water borne pathogens. Boating activities have increased in recent years with large numbers of kayakers now using the bay with limited waste facilities to meet their needs. There are a few live aboard vessels moored in the bay and there are two marinas. 2.1.4 Human health risks associated with water borne pathogens In May of 1998 there was an illness outbreak associated with the consumption of oysters from Tomales Bay. This event was linked to human virus that came from human sewage released into Tomales Bay. A preliminary survey of houses along 7 miles of the east side shoreline of the bay was conducted. This survey found two houses within 1.5 miles of the harvest sites associated with the disease outbreak that might discharge directly into the bay. In 2000, an additional shoreline survey work was conducted by DHS along 35.5 miles of shoreline. A visual survey conducted on foot found no obvious signs of failing septic systems or discharges to the surface of Tomales Bay (TBSTAC, 2001). No conclusive evidence was found as to the source of contamination. Shellfish harvested at the time that the contaminated oysters were collected met both the water and shellfish fecal coliform standards. In 2000, four cases of food borne illnesses associated with Vibrio parahaemolyticus prompted DHS to issue warnings to consumers against eating raw or undercooked oysters (Commandatore, 2000). V. parahaemolyticus is a naturally occurring halophilic (salt-requiring) bacterium that inhabits the coastal waters of the United States and is present in higher numbers during the summer. These food borne illnesses resulted in a cooperative monitoring plan between DHS and the shellfish growers. Weekly samples are collected between May and September of each year. In 2001 there were no sampled tissues detected as contaminated with V. parahaemolyticus in oysters from Tomales Bay. The event of human pathogens contaminating Tomales Bay oysters during times when the coliform standard was met in both the water column and in shellfish tissue brings into question the validity of fecal coliform as the sole indicator of safe conditions for harvesting. While monitoring for selected pathogens, as is now done in Tomales Bay, focuses on a known virus it does not assure that the tissue is safe from other forms of human pathogens. Tomales Bay Watershed Stewardship Plan: A Framework for Action 91

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This same argument can also apply to concerns that some pathogens from animal waste could affect humans since reduced fecal coliform still does not protect humans. As long as fecal coliform is the indicator used for public health and water quality standards (FDA, 2000), animal agricultural sources will merit management attention (Lewis et al., 2001). Since there is no simple or routine test to separate human pathogens from fecal coliform measurements and thus, there is no simple way to determine what percentage of the fecal coliform levels come from different sources the use of this standard will no doubt continue. As one of the early studies pointed out (Jarvis et al., 1978) it is unlikely that Tomales Bay will ever meet coliform objectives for shellfish harvesting during periods of substantial rainfall runoff even if all the dairies met the RWQCB Minimum Guidelines. While we know more about coliform sources now than in 1978 information is still lacking as to the role natural sources (e.g., large, over-wintering and resident bird populations, marine mammals) and the extent of human waste input (failing septic systems, boat and recreational uses) play in this process. These concluding statements are not intended to indicate that efforts should not continue to address fecal coliform but to warn that additional efforts to understand sources is necessary. These recent incidents of human illness caused by oysters collected while meeting current fecal coliform standards have been taken into consideration in forming thresholds for pathogen TMDLs. Based upon the current status of pathogen contamination in Tomales Bay and adjacent tributaries, the RWQCB has proposed numeric targets for the TMDL. The board staff has proposed using three different numeric targets: 1)the fecal coliform objectives for water found in the RWQCB Basin Plan to protect shellfish harvesting; 2)the fecal coliform shellfish tissue standard used by DHS to determine if shellfish have been contaminated by fecal waste and used by FDA as a market standard; and 3)zero discharge of human waste in order to protect the public from human viruses. 2.1.5 Trends in Bacterial Contamination Trend analysis of bacterial contamination is difficult because the data generated by many of the studies is not comparable. Time of year, level of effort, station locations, rainfall variability, stream flow data and rainfall records were not consistent between investigations making trends difficult to detect. An attempt was made in the TMDL report (Taberski, 2000) to make comparisons of fecal coliform results between studies. The author found many of the same problems of data incompatibility or incomplete data, however some trends were described. Because of the variability of the data only the highest, lowest, and median fecal coliform values were used from each study. Data from the 1995-96 pre and post-wet period samples were not included in the trend analysis. Four stations were selected from the watershed (Walker Creek, Millerton Creek, Grand Canyon Creek, and Olema Creek) and four stations from Tomales Bay (Walker Creek Delta, Marconi Cove, Blake’s Landing and Tomales Bay Oyster Company). Because of the issues discussed above, it was difficult to make any clear conclusion about fecal coliform trends over the years from 1974 to 1996. However, stations in the bay indicated that fecal coliform was lowest in the low rainfall years and that over the past twenty years levels of fecal coliform have stayed high during moderate to high rainfall periods, especially at the Walker Creek and Tomales Bay Oyster Company locations. Over the long term there were no clear overall trends of increasing or decreasing fecal coliform levels at watershed stations with the exception of Millerton Creek where Tomales Bay Watershed Stewardship Plan: A Framework for Action 92

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coliform levels increased over the time period represented by the studies. Later studies conducted on streams in the Lagunitas Creek and Olema Creek sub-watersheds (Ketcham, 2001) indicated that runoff from Olema Creek was one of the lowest fecal coliform loading streams flowing to the bay of the streams assessed. 4.0 Nutrients Tomales Bay was listed as impaired under the Clean Water Act section 303(d) (RWQCB, 1995) due to elevated nutrient levels in the tributary streams. At first glance a review of the existing data suggests that this nutrient impairment determination seems to be closely related to the high levels of total and fecal coliform in streams and the bay associated with animal agriculture and potentially failing septic systems. However, a recent study indicates that nutrient loading and more specifically, their fate and transport, may not be as closely associated with fecal coliform as first thought (Lewis, 2001). Nutrient loading needs to be investigated as an issue separate from fecal coliform. Most of the studies of tributary streams to date have concentrated on coliform with some nutrient measurements made but with little analysis of the results or understanding of their direct impact on Tomales Bay. Nutrient levels and their transport to the bay are likely closely linked to sediment movement. For example, phosphorus may be bound to fine particles and moved down stream with sediment to the bay. Emphasis has often been placed on monitoring total and un-ionized ammonia levels that have a direct and rapid effect on aquatic organism in the stream systems. Nitrogen and phosphorus do not necessarily have a direct effect upon entering the aquatic system but are nutrients that concentrate over time in the water column and sediments where they interact with other chemicals and can effect plankton production and benthic flux at a later time. Because balanced nutrient levels are critical in maintaining the bay ecosystem, it is important to distinguish natural levels from elevated concentrations coming from animal and human activities in the watershed. This is not a simple tasks since nutrient levels often involve complex relationships between sediment and the water column, storage in ponds and sediment sinks and seasonal variability. 4.1 Literature Summary on Watershed Nutrient Levels A number of recent watershed studies have taken measurements of nutrients although the emphasis was on other water quality factors. The most extensive study seems to be focused on the effects of animal agriculture on Tomales Bay tributaries (Lewis et al,. 2000; Lewis et al., 2001). This study found that mean total nitrogen concentrations/loads, ammonium concentrations/loads, nitrate instantaneous load, and phosphate concentration/loads for the control sites and sites upstream of agricultural facilities were not significantly different. Mean total nitrogen, nitrate and phosphate concentrations were significantly greater downstream from facilities than were the concentrations at the control watershed. Mean ammonium concentration downstream was not significantly greater than the control. Mean nitrate and phosphate levels were significantly greater downstream from the facilities.

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Studies conducted in the Lagunitas Creek Watershed by the NPS found that nutrients and ammonia were not a concern in this watershed (Ketcham, 2001). Nearly all of the samples collected from the larger stream systems, and most of the tributary samples were below detection limits. As Lewis observed, the nutrient cycling within the watershed must be better understood (Lewis et al., 2000). This cycling includes plant uptake, soil microbial and chemical processes and exchanges with the atmosphere. There is some indication from these two studies that nutrient loading from animal agriculture may not be as high as previously indicated (RWQCB, 1995; Lewis et al., 2000). Nutrient concentrations in the ground water were determined through extensive well sampling; groundwater discharge was estimated using both Darcy’s Law calculations and soil moisture budget. Results indicate that ground water discharge is of the same order of magnitude as summer stream flows. Dissolved nutrients concentrations in groundwater were consistently higher than surface water discharges (Oberdorfer et al., 1990). 4.2 Nutrients in Tomales bay Tomales Bay has been subjected to intensive study on water quality, bay water mixing and nutrient dynamics through the National Science Foundation, Land Margin Ecosystem Research (LMER) program (Kimmerer et al., 1993; Joye and Hollobaugh, 1995; Largier et al., 1997). This large data set provides an excellent understanding into the complex nutrient cycling found in estuaries. Tomales Bay is influenced by water exchange with the coastal ocean. Coastal seawater composition shows significant variation over an annual cycle, largely because of varying strength of coastal upwelling (Smith and Hollibaugh, 2000). Direct inorganic nutrient delivery from upwelling is not of major importance to the bay, but may be important indirectly by effecting nutrient dynamics within the bay. Particulate organic matter is delivered to the bay by tides and particle settling. Ecosystem respiration appears to exceed primary production by about 10 percent (Smith and Hollibaugh, 1997). This implies that the net ecosystem metabolism of the bay is supported to a significant extent by the import and oxidation of organic matter produced outside the system. The organic matter supporting the net heterotrophy of the bay (Smith and Hollibaugh, 2000) comes from land (about ½) and from the coastal ocean (the other ½). The activity of filter feeders (e.g., oysters and mussels) can alter the composition of available nutrients in the water column, impacting phytoplankton based food webs. Excreted material from large populations of bivalves may be returned to nutrient cycling systems, in such forms as NH4, which is readily taken up by bacteria (Judah, 2000). Eutrophication has been defined as an increase in the rate of supply of organic matter to an ecosystem. Studies in 1985-1986 indicated that spatial and temporal variations in primary productivity were similar to variations in phytoplankton biomass. During summer months productivity was highest in the seaward and central regions of the bay and lowest in the shallow landward region (Cole, 1989). This lack of sustained high phytoplankton concentrations suggests that the shallowness of the southern region, its shallow photic depths, wind-induced turbidity and feeding of benthic organisms keeps the populations at a lower level than other parts of the bay (Cole, 1989). Research has shown that the external supply of organic matter to Tomales Bay varies over seasonal and annual time scales (Chambers, Tomales Bay Watershed Stewardship Plan: A Framework for Action 94

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2000; Lewis et al., 2000). The rates of external inputs of organic matter to Tomales Bay may change in the future in response to regional changes in land use and/or the response to climate-driven changes in the watershed, estuary, and ocean complex. Internal generation of organic matter in the bay (algal blooms) could be stimulated by increased runoff of dissolved or sediment attached inorganic nutrients. The current state of the bay remains fairly pristine with the major impact of terrestrial runoff being the sediment transport and infilling of the bay (Chambers, 2000; Lewis et al., 2000). However, little is known about the phytoplankton dynamics in Tomales Bay and the shifting location of the maximum chlorophyll-a concentrations at different times indicates the dominant processes controlling phytoplankton biomass vary (Cole, 1989). Thus, more effort is needed in understanding primary productivity in Tomales Bay before much can be said about winter nutrient loading and summer algal growth as contaminants problems in the bay. 4.3 Nutrient Level Status and Trends A review of the current literature indicates that the nutrient levels in the watershed could be elevated but the database is not very extensive. There is some indication that nutrient loading from animal agriculture may not be as extensive as once thought. Additional studies on nutrient transport to the bay from agricultural operations needs to be completed before a clear understanding of the role of agriculture in nutrient enrichment is obtained. It is important to understand nutrient (C, N, P) reservoirs to clarify how this system responds to the influences of cattle and humans (Freifelder et. al., 1998). As the authors conclude understanding the linkages between land and water remains incomplete if fluxes from the land to the ocean are treated as outputs from a black box whose contents and internal reaction characteristics are unknown. Tomales Bay shows no indication of eutrophication with the current level of nutrient input from the watershed (Cole, 1989; Chambers, 2000; Lewis et al., 2000). Time series sampling was undertaken to describe seasonal, annual and interannual variations of fluxes of C, N and P over 8 years (1987-1995) by the LMER. (Smith and Hollibaugh 2002). They observed that the ocean in general and many systems in the coastal ocean in particular tend to oxidize more organic carbon than they produce. Tomales Bay is an example of this phenomenon called “net heterotrophy”(production: respiration ratio). The does not imply a low rate of primary production, but rather that respiration tends to exceed primary production. With so little seasonal data on nutrient loading from the watershed and nutrient levels in Tomales Bay trends cannot be determined. In addition, most of the 12 water quality studies conducted in the watershed and bay have emphasized total and fecal coliform measurements and not nutrient levels. While a large number of scientific papers address various monitoring results, hydrological models and geochemical reconstruction there remains limited data on eutrophication or the extent of anthropogenic nutrient loading from the watershed to Tomales Bay. 4.0 Toxic Contamination This section discusses toxic contamination found in bivalve tissue (both heavy metals and synthetic organics), mercury contaminated sediments and toxicity found in some sediments from Tomales Bay. Ammonia toxicity has been discussed in the section on nutrients only Tomales Bay Watershed Stewardship Plan: A Framework for Action 95

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because it is frequently determined from the same samples as those collected for nutrient analysis. 4.1 Bivalve Tissue Concentrations Sporadic data on toxic contamination has been generated primarily because the bay has been and is still being used as a control site. Unfortunately, the data generated from control sampling programs does not provide us with long-term, uninterrupted information on toxic contamination levels in Tomales Bay. The sampling protocols often reflect the needs of programs studying San Francisco Bay or other estuaries and do not address the needs of a Tomales Bay database on potential toxic contaminants. The best archival data sets that we have on Tomales Bay water column toxic contaminate levels is from the California Mussel Watch Program, the National Mussel Watch Program and the San Francisco Bay Regional Monitoring Program (SFEI). More recently the RWQCB has taken bivalve tissue samples from suspended organism (5 year period) to study uptake of mercury (Whyte, 2002) although the data has not be published. These programs used bivalves as an organism to bioaccumulate contaminants from the water column over time. Both transplanted and resident bivalves have been used as control organisms for toxic uptake studies in other bays. Both heavy metals and anthropogenically produced organic compounds were analyzed in the tissues of the test organisms. See Appendix F: Bivalve Tissue Concentrations for additional information. 4.2 Mercury Contaminated Sediment The Gambonini mercury mine was operated from 1964 to 1970 and generated over 300,000 m3 of waste with an average concentration of 320 ng/kg of mercury that was dumped on the slope at the mine site (Whyte, 2000). Approximately 5000 flasks of mercury were extracted from the high-grade cinnabar deposits. In an attempt to reduce mine waste discharge and protect water quality, the mining company constructed a dam 400 meters downstream from the waste pile. By 1990 the dam failed and mass wasting occurred down slope releasing the waste material into a tributary stream of Walker Creek (Whyte, 2000). In order to mitigate the mercury transport from the mine site, the USEPA and the San Francisco RWQCB an emergency Superfund Cleanup in 1998 (Whyte, 2000). Water column samples were collected and analyzed. Total mercury concentrations ranged from 485 to 1,040,000 ng/l exceeding the water quality objective of 12 ng/l. Much of the mercury laden deposits may potentially be stored along Walker Creek and in the salt marsh and the sediments of the Walker Creek delta while some mercury contaminated sediments may have moved down bay. Studies conducted by Whyte and Ganguli measured mercury concentrations in the Walker Creek delta as high as 13 ppm in 1999. During studies in 2000, 11 sites were sampled in the Walker Creek Delta where individual samples ranged from 7.6 to 0.06 ppm (Whyte, 2000). Methylmercury concentrations (a highly toxic organic form) were not correlated with high mercury concentrations. Methylmercury concentrations averaged 0.0015 ppm and ranged from 0.0114 to 0.00001 ppm. Much of the data collected during the mercury sediment studies has not been completely analyzed and/or the quality control review has not be completed, thus, this data is not ready for public review at this time (Whyte, 2002). Tomales Bay Watershed Stewardship Plan: A Framework for Action 96

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In addition to the sediment measurement, a number of bay invertebrate tissues were also analyzed for mercury. Resident bivalves (cockles) collected in the sediments of Walker Creek delta contained up to 0.34-ppm (wet wt.) mercury while cockles harvested at McDonald sampling site (11 km south of Walker Creek) contained only 0.055 ppm mercury (Whyte and Kirchner, 2000). This fact may indicate that the down bay transport of contaminated sediment has not moved quickly. Mercury concentrations in commercial oysters were also measured and ranged from 0.029-0.049 ppm, below FDA action levels. These tissue values compare to the levels reported by the San Francisco Bay Institute’s Regional Monitoring Program that also used oysters from Tomales Bay. As Whyte and Ganguli (2000) point out the oysters are feeding out of the water column and have lower levels than mollusks (cockles and mud snails) that are in direct contact with the contaminated sediment. In addition to molluscan tissue, the burrowing ghost shrimp (Callianassa californiensis) was also sampled and contained relatively high mercury levels (0.39-0.45 ppm). Shore crabs (Pachygrapusus crassipes) from the Walker Creek Delta area had 6 times more mercury than shore crabs from McDonald. An early study in 1973 (Swanson, 1973) of mercury accumulation in the purple shore crab (Hemigrapsus nudus) measured mercury levels in the near shore water column just North of the mouth of Tomales Bay and found mean levels of 0.24 ppb. These values most likely reflect the natural background levels in Bodega Bay at that time. The ten most commonly caught and consumed fish species from Tomales Bay were collected and the tissue analyzed for mercury (Whyte and Kirchner, 2000). Mean mercury concentrations were highest in brown smooth hound sharks (1.31 ppm wet wt.) and leopard sharks (1.09 ppm), followed by bat rays (0.56 ppm), angel sharks (0.43) with lower levels in halibut, redtail surf perch, shiner surf perch and jack smelt. These results instigated an interim public health advisory for sport fish from Tomales Bay (MCDHHS, 2000). The advisory recommendations included not eating leopard and brown smooth hound sharks and limited consumption of surfperch, halibut, pacific angel sharks and bat rays. Because many of these fish species do move around and some leave the bay for undetermined time periods it is more difficult to directly relate the mercury concentrations in Tomales Bay sediments with the tissue burden of these fish species without more research. These types of advisories often raise public concerns and also result in added questions about the findings (Baty, 2000), as mercury values in some of the fish sampled in the San Francisco Bay estuary in the Food and Drug Administration’s national sampling had comparable mercury levels. A study of mercury and selenium in diving ducks from the San Francisco Bay region used Tomales Bay as a reference site (Hoffman et al., 1998). Both the greater scaup and surf scoters collected from the site were found to have elevated hepatic mercury concentrations. These differences correspond to higher mercury levels found in sediments from Tomales Bay than from sites in San Pablo Bay near Suisun Bay (Long et al., 1990). Both species of ducks feed on shellfish and crabs and migrate from more northern locations to over winter along the west coast (Udvardy, 1985). While the authors indicate that the higher mercury concentration in Tomales Bay sediments may play a role in the elevated hepatic levels in the ducks studied, direct connection is difficult with these migratory duck species since part of their time is spent feeding in other areas that could have mercury in bivalves or sediment. Tomales Bay Watershed Stewardship Plan: A Framework for Action 97

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Also information is lacking on the pathway of mercury through the food web that the ducks are using. 4.3 Unknown Source of Sediment Toxicity Toxicity tests were conducted on homogenized Tomales Bay sediments collected at Marconi Cove (Hunt et al., 1998). This site was selected as a reference for evaluating the toxicity of San Francisco Bay sediments. Survival of the amphipod Eohaustorius was found to be poor when the Tomales Bay sediments were tested. The Tomales Bay site had the highest percentage of clay particles, among the reference sites used in the study, with greater than 69 percent of the sample mass composed of particles less than 4 µm. In a comparative study between San Francisco Bay and Tomales Bay sediments several of the test endpoints for three samples from Tomales Bay were among the most toxic (Long et al., 1990). The location of the Tomales Bay samples were near 38o09’02”N, 122o53’55”W which was located in the vicinity of the Marshall Boat Works and close to the TB-WC-mid station sampled by Whyte and Kirchner (2002). The samples were collected from a boat using a 0.1 m2 Young grab sampler with the upper 1 cm taken from the surface of 6 to 10 samples at each station. Several of the endpoints used in the toxicity tests, for example, the mussel M. edulis and echinoderm S. purpuratus showed abnormal development and the survival of the amphipod R. abronius was below control values. As the authors state, these results are not easily explained. The concentrations of chromium and nickel in two of the samples were elevated relative to the other sites in the study. The other chemicals analyzed in the Tomales Bay samples were not elevated. Benthic samples collected synoptically with the sediments tested were dominated by hardy polychaetes and mollusks with an absence of more sensitive crustaceans that might indicate some level of toxicity. Using a model (DeWitt et al., 1988) for interpreting the results of measuring R. abronius survival in uncontaminated fine-grained sediments did not account entirely for the toxicity observed. Based on the outcome of these two studies the cause of the relatively inhospitable sediment from parts of Tomales Bay remains unsolved and is due to some unknown factor(s) (Long et al., 1990). Based upon these results and reference sites identified within San Francisco Bay the use of remote reference sites like Tomales Bay has diminished (Hunt et al., 1998). 4.4 Status of Toxic Contamination Unfortunately, the bivalve tissue data is not continuous, with wide gaps and few water column measurements to relate to the uptake values found in the tissue samples. Data collection in Tomales Bay has been reduced as the bay is less frequently used as a reference site for studies in San Francisco Bay. More recently the RWQCB has deployed bagged bivalves for 5 years as part of the mercury studies. At the present time there is very little data being gathered on trace element and synthetic organic compounds in sediments or in the water column in the Tomales Bay with the exception of mercury. See Bivalve appendix for additional information.

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4.5 Trends in Toxic Contamination Transplanted and resident bivalves are valuable in the assessment of long-term trends because they provide an integrated measure of contamination over a three month period (normal transplant time) or longer for resident samples. This interval is more appropriate for the assessment of interannual trends than the one-hour representation of a water column grab sample or the longer-term sediment accumulation period (20+ years). No trend analysis or formal evaluation of the data was conducted for this narrative. Some general statements can be made as to visual trends taken from the figures presented in Appendix F. Mercury levels have remained low both in oyster and mussel tissue collected from Tomales Bay in all the years sampled. Cadmium levels were elevated in 1994 in oysters and then have steadily declined through 2000. The same trend can be seen in cadmium levels in mussel tissue. Nickel increased in mussel tissue in 1997 while declining in 1998. Nickel in oysters has remained low during the more recent sampling periods. Copper levels in oysters have declined from 1997 to 2000, while manganese has increased in recent years in mussel tissue. These elevated manganese levels may reflect increased sediment loads coming from old mining operations or maybe a byproduct of sediment movement out of the watershed in general. Manganese in not particularly toxic to aquatic life and is slowly precipitated as a dioxide as it reacts with dissolved oxygen. Synthetic organics are low in bivalve tissue from Tomales Bay, however, the fact that toxic, persistent synthetic organochlorine compounds including polychlorinated biphenyls (PCBs), and dichloro-diphenol-trichloroethane (DDT) and dieldrin have been recorded indicates that they are present in the watershed. Polycyclic aromatic hydrocarbons (PAHs) have increased in recent years to a high in 1998. This change might suggest that boat traffic has increased with more petroleum products entering the Bay. The butylin products have declined from a high in 1994 to very low levels in 1998. This fact may indicate that the removal of this compound from antifouling paints has reduced available levels for bioaccumulation. Metal and synthetic organic contaminants in bivalve tissue still generally remain low. However, at various points in time, levels have been high when compared to other west coast regions. The fact that these contaminants can bioaccumulate in Tomales Bay bivalve tissue is a strong argument for continued assessment. 5.0 Sediment Loading in Tomales Bay Sediment loading from tributary streams into Tomales Bay is addressed in the Human Uses section this plant. However, some discussion is warranted because sediment is often a carrier of toxic chemicals, coliform bacteria and nutrients. Sedimentation is rapidly occurring in Tomales Bay. Comparisons were made between 1861 and 1957 using hydrographic charts with corrections made for changing sea levels (Rooney and Smith, 1999). These calculations showed a bay wide average infilling rate of 5mm/yr. This is equivalent to a watershed Tomales Bay Watershed Stewardship Plan: A Framework for Action 99

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erosion rate of approximately 80,000 tons per year. The largest sediment influx seems to have occurred between about 1930 and 1960. The physical filling of the bay reduces the water volume, alters circulation patterns, changes nutrient levels, effects benthic communities and estuary habitat in general, and it also can effect the contaminate load in the bay. As previously discussed, mercury attached to fine particles has and most likely will continue to move into Tomales Bay. Phosphate and coliform bacteria can be attached to particles and also be transported and deposited into bay sediment. Re-suspension can occur during high winds and winter runoff, thus exposing the system to new pulses of contaminates. 6.0 Data Gaps The recommendations in this section are intended to identify gaps in information and suggest methods and studies to fill these gaps for future consideration and planning by the Council and other partners in the Tomales Bay watershed. These recommendations are not to be confused with the Action Plan, but rather to guide future planning activities and discussion. 6.1 Watershed and Bay Wide Monitoring In order to establish a baseline of present conditions in Tomales Bay and tributaries a water quality monitoring plan should be designed to follow important parameters through time. Based upon existing data, stations could be selected to monitor temporal and spatial changes in the bay. Water flow from the tributaries along with water quality parameters would provide important information on watershed changes. This program could include measurement for nutrients, salinity, temperature, suspended solids, suspended particulate matter, dissolved oxygen, light penetration and chlorophyll concentrations. With new techniques many of these parameters can be measured directly with an automated CTD instrument package. These basic elements of water quality define the suitability of the bay as a habitat for marine life and for the support of aquaculture. See item 2.0 in the Action Plan for additional information on the development of a Comprehensive Water Quality Monitoring Program for Tomales Bay. 6.2 Specific Recommendations for Consideration in the Development of a Comprehensive Water Quality Monitoring Program for Tomales Bay Because the TMDL process will be driving a number of studies related to designated contaminants it will be important to collect the necessary information to select thresholds that are protective to beneficial uses but not prohibitive to legitimate uses of the bay and watershed. The TMDL analysis can be divided into four components: source analysis, loading capacity estimates, development of numeric targets and load allocations. Some indications of data needs can be addressed by describing the Total Maximum Daily Load as: TMDL =ΣWLAs +ΣLAs + NB Where: Σ= the sum, WLAs= waste load allocations, Las= load allocation and NB= Natural Background. The data gaps outlined in this narrative Tomales Bay Watershed Stewardship Plan: A Framework for Action 100

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address information that is simply missing, information needed for the TMDL process, or data that, if collected, could provide a better understanding of the bay and watershed. Some of the recommendations are based on input from agency reports (Taberski, 2000; Lewis et al., 2001; RWQCB, 2001), research studies and observations based on this review. The RWQCB has developed recommendations for study and monitoring programs (SWAMP) for Walker Creek and Lagunitas Creek watersheds (RWQCB, 2001). 1. Develop a monitoring program to study nutrient, pathogens and sediment movement in Keys, Chileno, Arroyo Sausal, Salmon, and Walker Creek to evaluate the effects of grazing. 2. Develop a monitoring program for pathogens and nutrients at Laguna Lake to determine the input from the headwaters of Chileno Creek. 3. Develop a monitoring program for pathogens and nutrients below the town of Tomales to evaluate the septic system leaks into Keys Creek. 4. Develop a monitoring program to evaluate the impact of flow, temperature, dissolved oxygen and sediment on the salmonid fishery below Soulajule Reservoir. 5. Design a sampling program above Peters Dam to establish reference conditions in a protected upper watershed for flow, temperature, dissolved oxygen, and biological indicators. 6. Develop a monitoring program to evaluate water quality (DO, temp. and sediment) in Lagunitas Creek below Peters Dam, in Nicasio Creek below Seeger Dam and San Geronimo and Olema Creeks. 7. Develop a monitoring program for sediment deposition up and downstream from the confluence of Lagunitas and San Geronimo Creeks to evaluate erosion control programs. 8. Monitor for pathogens and nutrients from septic tank leaks along San Geronimo Creek. 9. Conduct nutrient and pesticide testing below the golf courses on Bon Tempe Lake and on San Geronimo Creek. 6.3 Conduct focused studies to gather information on water borne pathogens in Tomales Bay and tributary streams. The database on bacterial contamination in the bay and watershed is well developed but there are still a number of data gaps that include: 1) contributions made by natural background sources (e.g., large, over-wintering and resident bird populations, marine mammals) and the extent of human waste input (e.g. failing septic systems, boat and recreational uses) into the watershed and bay; 2) comparative studies of the eastern shoreline sub-watersheds that have low fecal coliform counts with those sub-watersheds that have high fecal coliform levels in order to establish background conditions; 3) address the concern about increases in summer primary productivity in Tomales Bay by designing studies to determine spatial and temporal dynamics of phytoplankton in the various sections of the bay. A. Compare land use practices and water sources that exhibit high bacterial counts with those practices and sources that show low level counts. B. Continue to pursue the identification of sources of fecal contamination in the watershed and develop a priority list and action plan to reduce the bacterial levels. Tomales Bay Watershed Stewardship Plan: A Framework for Action 101

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C. Investigate the use of DNA fingerprinting, protein tagging techniques along with other indicator studies to determine specific sources of bacterial and viral (where possible) contamination. D. Develop a study program to determine concentrations, movement and longevity of human pathogens in Tomales Bay. E. Develop a monitoring study to identify specific point sources of fecal coliform in the watershed in order to develop specific remediation activities. F. Investigate the role of natural levels of fecal coliform, sources, abundance and possible reduction methods in relationship to shellfish harvesting. G. Continue studies that contribute to our knowledge of animal agricultural operation methods that reduce fecal coliform levels in tributaries. H. Continue investigations to observe water quality outcomes from the timing of grazing such as winter use and the proximity of pastures to waterways. I. Develop a study plan to estimate the bacterial contribution of marinas, resident live aboard vessels, day use and visiting vessels, commercial fishing boats and ways to control discharges. J. Develop study plans to investigate possible sources of human pathogens from malfunctioning septic systems along the shores of Tomales Bay and tributaries. K. Encourage a study program by state and federal park management to evaluate existing waste collection facilities for day use, overnight camping and boating needs and to make the necessary corrections. 6.4 Conduct focused studies on nutrient levels in Tomales Bay and tributary streams. Evaluation of nutrient levels is far behind monitoring activities related to bacterial contamination. As stated earlier in this report more effort is needed to really understand primary productivity in Tomales Bay. The role of nutrient runoff in winter and the perceived increase in primary productivity (lower end of the bay) in the summer should be investigated to determine if the concern is really a problem and if it does occur, to establish the spatial and temporal patterns. A limited number of studies have collected nutrient concentration data and much of that was aimed at determining toxic level of ammonia. Thus, this area of investigation should consider the following major data gaps: A. Conduct studies in the Lagunitas and Walker Creek watershed to determine the level of year around nutrient loading into tributary streams from surface and groundwater sources. B. Where high levels are found develop a monitoring program to determine source, transport times, nutrient chemical mixtures and levels that reach the bay from the contaminated tributaries. C. Determine reference systems to investigate and compare nutrient background levels with suspected contaminated sites. D. Develop studies to determine the levels of nutrients (carbon, nitrates, nitrites, phosphates, ammonia) that are really reaching the bay. E. Through modeling and/or direct measurements establish levels that are likely to cause eutrophication or other problems from nutrient loading in Tomales Bay waters. Tomales Bay Watershed Stewardship Plan: A Framework for Action 102

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F. Investigate the role of shellfish growing on the fate of excreted nutrients, nutrient cycling patterns and the effects of ingestion of phytoplankton by concentrated bivalve cultures on bay waters. G. Support ongoing efforts by the animal agricultural groups to better understand nutrient loading, monitoring of runoff patterns and control processes. 6.5 Assess toxic contamination in Tomales Bay and tributary streams. Most of the effort to understand toxic contamination has been centered on mercury released from the Gambonini mine in the Walker Creek watershed. On-going and future studies will fill some of the data gaps include: A. Continue to monitor the release of mercury from the mine site to determine the success of the remediation program. B. Evaluate mercury contaminated sediment transport out of the Walker Creek drainage into Tomales Bay. C. Investigate the storage of contaminated sediment in the drainage and estimate possible release times for pulsed levels of sediment reaching the bay. D. Continue the investigation of contamination pathways through various biological trophic levels in the bay system. E. Investigate the extent of contaminated sediment movement within Tomales Bay. F. Investigate the natural levels of mercury entering the bay system from the Lagunitas sub-watershed and other smaller tributaries. G. Develop a monitoring plan to examine the bioaccumulation of metals and synthetic organic compounds to establish a long-term baseline in Tomales Bay.

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Literature Cited Baty, T. 2000. Further thoughts on mercury in Tomales Bay. Point Reyes Light. Point Reyes, California. Bennett, R. H. 1992. Programs and Practices for the Protection of Tomales Bay. Third Biennial State of the Bay Conference, Inverness Yacht Club. Chambers, R. M. 2000. Tomales Bay - LMER/BRIE Studies 1987--1995. Fourth State of Tomales Bay Conference, Inverness Yacht Club. Clark, C., J.W. Nute, and P. Warshall. 1978. Cumulative Impact Study of Septic Tank Disposal Systems in the Inverness Area of Marin County, Cooper Clark and Associates and J. Warren Nute, Inc.: 74. Cole, B. E. 1989. “Temporal and Spatial Patterns of Phytoplankton Production in Tomales Bay, California, USA.” Estuarine, Coastal and Shelf Science 28: 103-115. Commandatore, M. 2000. Triennial Sanitary Survey Update Report:2000, California Department of Health Services: 5. Daetwyler, C. G. 1966. Marine Geology of Tomales Bay, Central California, Scripps Institution of Oceanography and Pacific Marine Station: 169. DeWitt, T. H., G.R. Ditsworth, and R.C.Swartz. 1988. “Effects of natural sediment features on survival of the Phoxocephalid amphipod, Rhepoxynius abronius.” Marine Environmental Research 25: 99-124. California Department of Health Services (DHS). 1996. Identification of Sources of Bacterial Indicators of Water Quality of Tomales Bay Shellfish Beds, Pilot Monitoring Program, Winter 1994-95, California Department of Health Services, Environmental Microbial Diseases Laboratory. Freifelder, R., Smith, S.V., and R.H. Bennett. 1998. Cows, humans and hydrology in the nitrogen dynamics of a grazed rural watershed. Journal of Environmental Management Volume: 52(2): 99 - 111. Hoffman, D. J., H.M. Ohlendorf, C.M. Marn, and G.W. Pendleton. 1998. “Association of Mercury and Selenium with Altered Glutathione Metabolism and Oxidative Stress in Diving Ducks from the San Francisco Bay Region, USA.” Environmental Toxicology and Chemistry 17(2): 167-172. Hultquist, R. H. 1982. Tomales Bay Sanitary Survey. Santa Rosa, Department of Health Services,: 24. Hunt, J. W., B. S. Anderson, B.M. Phillips, J. Newman, R. Tjeerdema, M. Stephenson, M. Puckett, R. Fairey, R.W. Smith and K. Taberski. 1998. Evaluation and Use of Sediment Reference Sites and Toxicity Tests in San Francisco Bay, California State Water Resources Control Board, California Department of Fish and Game, Institute of Marine Sciences: 246. Jarvis, F. C. N., M. Ammann, and M. Yee. 1978. Tomales Bay and Watershed Water Quality Surveys During 1976-77 and 1977-78, San Francisco Bay Regional Water Quality Control Board: 33. Joye, S. B. and J.T. Hollibaugh. 1995. “Sulfide inhibition of nitrification influences nitrogen regeneration in sediments.” Science 270: 623-625. Judah, L. R.. 2000. Filtering Capacity and Dietary Requirements of the Pacific Oyster, Crassastrea gigas, San Francisco State University: 7.

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Kelly, J. P., J.G. Evens, R.W. Stallcup, and D. Wimpheimer. 1996. “The Effects of aquaculture on habitat use by wintering shorebirds.” California Dept. of Fish and Game 82(4): 160-174. Kelly, J.P. and K. Etienne. 1999. Inventory of winter waterbirds and shorebirds on Tomales Bay, 998-1999. A report to the Point Reyes National Seashore. ACR Technical Report #89-12-5, Audubon Canyon Ranch, Marshall, CA 94940. Ketcham, B. J. 2001. Point Reyes National Seashore Water Quality Monitoring Report-May 1999-May 2001, National Park Service--Point Reyes National Seashore, Water Quality Monitoring Program: 177. Kimmerer, W. J., S.V. Smith, and J.T. Hollibaugh. 1993. “A simple heuristic model of nutrient cycling in an estuary.” Estuarine, Coastal and Shelf Science 37: 145-159. Largier, J. L., J.T. Hollibaugh, and S.V. Smith. 1997. “Seasonally hypersaline estuaries in Mediterranean-climate regions.” Estuarine, Coastal and Shelf Science 45: 789-797. Lewis, D., K. Tate, D. Atwill, E. Rilla, S. Larson, D. Ghirardelli, and P. Olin. 2000. System Assessment to Improve Water Quality Management on Agricultural Lands. Fourth State of Tomales Bay Conference, Inverness Yacht Club. Lewis, D., M. Lennox, R. Atwill, K.Tate, S. Larson, P. Olin, and E. Rilla. 2001. Tomales Bay Water Quality Project Update. U.C, Cooperative Extension: 31. Long, E. R., M.F. Buchman, S.M. Bay, R.J. Breteler, R.S. Carr, P.M. Chapman, J.E. Hose, A.L. Lissner, J. Scott, and D.A. Wolfe. 1990. “Comparative Evaluation of Five Toxicity Tests with Sediments From San Francisco Bay and Tomales Bay, California.” Environmental Toxicology and Chemistry 9(9): 1193-1214. Marin County Department of Health and Human Services (MCDHHS). 2000. Interim Public Health Advisory for Sport Fish from Tomales Bay, Marin County Department of Health and Human Services. Musselman, J. F. 1980. Sanitary Survey of Shellfish Waters, Tomales Bay, California, February-Marsh 1980. Davisville, RI, Department of Health and Human Services, Public Health Service, Food and Drug Administration, Shellfish Sanitation Branch: 63. Oberdorfer, J. A., M.A. Valentino, and S.V. Smith. 1990. “Groundwater contribution to the nutrient budget of Tomales Bay, California.” Biogeochemistry 10: 199-216. Rooney, J. J. and S.V. Smith. 1999. “Tomales Bay, California, sedimentation rates and watershed landuse.” Journal of Coastal Research. Rugg, M. 1992. California Department of Fish and Game: Activities and Plans. Third Biennial State of the Tomales Bay Conference, Inverness Yacht Club. Rugg, M. 2000. Marin-Sonoma County Agricultural Runoff Influence Investigation 19992000 Summary, California Department of Fish and Game: 12. Rugg, M. 2002. Marin-Sonoma Counties Agricultural Runoff Influence Investigation 20002001 Summary, California Department of Fish and Game: 45. Regional Water Quality Control Board (RWQCB) 1995. Water Quality Control Plan, Beneficial Uses, Regional Water Quality Control Board, Region 2: 2-1 to 2-11. RWQCB. 2001. Surface Water Ambient Monitoring Program (SWAMP) Workplan 20012002. Sharpe, C. A. 1974. Tomales Bay Shellfish and Water Quality Study, Water Sanitation Section, California State Department of Health: 206.

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Smith, E. H., R.G. Johnson, and S. Obrebski. 1971. Physical, Chemical, Microbiological and Hydrographic Characteristics of Tomales Bay, Pacific Marine Station, University of the Pacific: 118. Smith, S. V. and J.T. Hollibaugh. 1997. “Annual Cycle and Interannual Variability of Ecosystem Metabolism in a Temperate Climate Embayment.” Ecological Monographs 67(4): 509-533. Smith, S. V. and J.T. Hollibaugh. 2000. The Tomales Environment, University of Hawaii, School of Ocean and Earth Science and Technology and San Francisco State University, Tiburon Center. 2002. Smith, V. and J.T. Hollibaugh. 2002. Tomales Bay, California (USA). Swanson, R. G. (1973). Some Aspects of Mercury Accumulation by the Purple Shore Crab Hemigrapsus nudus Dana (Crustacea: Decapoda). Graduate Studies, Pacific Marine Station. Stockton, California, University of the Pacific: 141. Taberski, K. 2000. Controlling Pathogens in Tomales Bay, California Total Maximum Daily Load: Background, Problem Statement and Numeric Targets, California Regional Water Quality Control Board San Francisco Bay Region: 29. Tomales Bay Shellfish Technical Advisory Committee (TBSTAC). 2001. Draft Twelve-year Sanitary Survey Report --Shellfish growing area classifications for Tomales Bay, California, Preharvest Shellfish Sanitation Unit, Department of Health Services: 36. Udvardy, M. D. 1985. The Audubon Society Field Guide to North American Birds. New York, Alfred A. Knopf. U.S. Environmental Protection Agency (USEPA). 1998. Methods of sampling and analyzing contaminants in fish and shellfish, USEPA. U.S. Food and Drug Administration (FDA). 2000. National Shellfish Sanitation Program Model Ordinance, 1999 Revision, US Food and Drug Administration, Office of Seafood: 12. Whyte, D. C. 2002. San Francisco Regional Water Quality Control Board. Whyte, D. C. and J. W. Kirchner 2000. “Assessing water quality impacts and cleanup effectiveness in streams dominated by episodic mercury discharges.” The Science of the Total Environment 260: 1-9. Whyte, D. C. and P.M. Ganguli 2000. The Impact of Mercury Mining on Tomales Bay Biota. EPA Mercury Conference.

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Appendix B. Erosion and Sedimentation in the Tomales Bay Watershed 1.0 Introduction Watersheds develop a mantle of soil and vegetation that resists erosion and is affected by climate, geology and land use (Zumwalt, 1972). The geology and geomorphic processes of a watershed influence its soil formation, freshwater flow, the composition of the streambed, erosion, and many other features that control the way it functions (Galloway, 1977; Evens, 1993). Erosion is a natural process that brings nutrients and beneficial substrates to aquatic ecosystems (Prunuske Chatham, Inc., Inc 2001). Accelerated erosion, however, caused by human disturbance, overloads water bodies with sediment and reduces their water capacity, causing areas such as streams, pools and wetlands to fill in, among other consequences. Human activities have altered the landscape of the Tomales Bay watershed, resulting in increased sedimentation and nutrient inputs and decreases freshwater inflow to the bay. These variables have a substantial effect on the physical, chemical, and biological processes in Tomales Bay and on the diversity of wildlife that inhabit its ecosystems. Erosion and sedimentation are significant factors in the decline of many wildlife species, and in the watershed have detrimentally affected the coho salmon and steelhead population of Lagunitas Creek, Walker Creek and its tributaries (Bratovich, 1984; Rich, 1989; Prunuske Chatham, Inc., 2001). 2.0 Erosion and sedimentation processes Vegetation cover has a significant effect on erosion. Primarily, it offers protection against runoff, rain and stream bank erosion by binding the soil with the roots and increasing its cohesion (UCCE, 1995). The lack of vegetation leaves the soil unprotected and decreases water infiltration, resulting in increased runoff and removal of surface soil particles. All erosion results in degradation of soil productivity as well as the sedimentation of streams, estuaries and bays. As described by Wahrhaftig & Wagner (1972), there are various erosional processes that affect the landscape of the Tomales Bay watershed. On the slopes of hills, erosional processes include: sheetwash and rainwash of bare soil; piping or the erosion of sediment by storm waters moving through cracks in the soil; rilling and gullying; landslides; debris flows; and the slow down-hill movement of a thin piece of mantle. This material eventually moves into the streams and is carried as bedload (gravel and sand) or as suspended sediment (fine sand, silt and clay), ultimately ending up in Tomales Bay or the ocean. Stream bank erosion is a particular problem in streams that lack riparian vegetation (UCCE, 1995). Because eroded material is deposited directly into streams and the bay it is a primary source of water quality and habitat degradation. Sediment may move directly into a stream from the land during a storm. The stream may store some of its sediment on its bank or in its bed and not deposit it all in the bay. During floods it may deposit some of the sediment on its floodplains

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and as the stream moves over the floodplain over the years, the sediment will erode, transforming the material it formerly deposited. Gullies result from concentrated water flow, often in areas lacking protective vegetation. They commonly result from poorly constructed or maintained roads. Unprotected culvert outlets, road drainage ditches that concentrate water flow, and roads where surface flow is not properly diverted, are common causes of gully initiation. Gopher tunnels and livestock trails in pastures can also initiate gullies (UCCE, 1995). Cultivated fields and overgrazed pastures are potential sources of sheet, rill, and gully erosion. 3.0 Water Diversions and Impoundments The construction of dams in the watershed has affected sediment transport in the creeks. Dams alter the movement of sediment through the stream system. Above the dam, sediment is prevented from moving downstream, and the composition of the substrate below a dam is often changed. Below dams streams can become depleted of needed sediment because the dams reduce the highest flows that would naturally occur, not allowing the stream to flush out the system and move sediment through the stream channel (Prunuske Chatham, Inc., 1997). Major impoundments in the Lagunitas Creek sub-watershed include: Kent, Alpine, and Bon Tempe Lakes, Lake Lagunitas and Nicasio Reservoir. Peters Dam holds 32,900 acre-feet in Kent Lake, about a mile downstream from the three smaller reservoirs near the headwaters, Lake Lagunitas, Bon Tempe Lake, and Alpine Lake. On Walker Creek, the largest reservoir to date is the Soulajule Reservoir (Marin County, 1981). While dams act as sediment traps for about 70 square miles of the Tomales Bay watershed, they can also stimulate downcutting of the channel down stream (UCCE, 1995; Prunuske Chatham, Inc., 1997). Dams affect sediment loading downstream of the dam, as well as change the composition of the sediment. Their most significant affect on the stream is the reduction in flood flows that can clean downstream areas and remove sediments. Apart from the effect of dams on sediment transport, the diversion of water out of the watershed has reduced freshwater flows. This reduces the nutrients entering the bay from the watershed and interrupts the natural freshwater flushing (California Coastal Conservancy, 1984). The lack of flushing flows means that sand and fine gravels are not transported, so excess bed sedimentation occurs. Temperature, oxygen, and bed composition are all affected by reduced flow, as is the concentration of pollutants and residues that might be present in the water. The reduced freshwater flow also reduced spawning habitat for salmonids. 4.0 Historical drainage changes in the watershed The earliest hydrographic surveys, from 1860 to 1861, show open water at the mouths of even the smallest creeks entering to the bay. Although some marshes are shown at the mouth of Lagunitas and Olema Creeks, they may have been formed by sediment influx due to logging and grazing in the watershed, prior to the survey. The hydrographic surveys also show deep water extending up the bay to Inverness and a navigable channel to Point Reyes Station. No marshes are shown at the mouth of Walker Creek and there was evidently a

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navigable channel to Tomales (California Coastal Conservancy, 1984; Evens, 1993) (Figure 1).

Figure 1. The southern portion of Tomales Bay as shown by hydrographic surveys in 1861 and approximately one hundred years later. (Source: California Coastal Conservancy, 1984; Evens, 1993). During the last 100 years, an increase in erosion in the upper-slope and valley regions of the Tomales Bay watershed, has caused increased sedimentation rates. This additional sediment allows for slow but continuous filling and subsequent shoaling of the southern half of Tomales Bay (California Coastal Conservancy, 1984; Evens 1993). Much of the excess sediment accumulates at the base of the watershed and in its valleys, marshes, deltas, estuaries and most dramatically in its head, which includes the mudflats and the Lagunitas Creek Delta. Since 1861, the Lagunitas Creek Delta has been slowly filling bayward, approximately 100 feet in the last 100 years (1-2 feet of sediment accumulation) (Storm, 1972). Niemi and Hall (1996) note that the most dramatic changes in the landscape of the watershed occurred between 1860 and 1918, with the rapid progradation of the tidal marsh of Tomales Bay. This period marks the denudation of the watershed with its resulting slope instability and erosion, reflected in the high sedimentation rates. During this period, siltation near the head of Tomales Bay caused the tidal marsh to move more than a kilometer to the northwest. Olema Creek also moved west during this interval. In 1862, only one tidal channel connected with Lagunitas Creek. During this period, 50,000 acres of the watershed was purchased and subdivided into ranches, major roads and railroad were built, and intensive logging occurred for redwoods in Lagunitas and Douglas fir in Olema, and on the Inverness Ridge. The construction of a railroad on the east side of Tomales Bay in the 1870’s isolated many small coves, causing them to fill with sediment and become vegetated with saltmarsh plants (especially pickleweed). Also, as a result of logging and increased grazing in the watershed, Tomales Bay Watershed Stewardship Plan: A Framework for Action 109

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more sediment was carried into Tomales Bay, Bolinas Lagoon, and the coastside estuaries, raising the elevation of the deltas and permitting saltmarsh vegetation to grow over former mudflats (Evens, 1993). During the period of 1918 to 1954 the alteration of the Tomales Bay watershed continued, as the marshland at the head of Tomales Bay prograded an additional 500 to 800 meters to the northwest. Part of the watershed was converted into pastures during this period, levees were constructed along inlets, and seasonal dams were also constructed in Lagunitas Creek. The headwaters of Lagunitas were dammed in 1919 to form Alpine Lake (Niemi and Hall, 1996). The drainage of the floodplain of Olema Creek and the marshlands at the southeastern end of Tomales Bay were especially modified by the creation of a 3 km long straight canal excavated between the town of Olema and the Levee Road. During the period of 1954 to 1982 no major drainage changes were observed to occur in the watershed (Niemi and Hall, 1996). Two additional reservoirs were built in the Lagunitas Creek drainage basin, Kent Lake in 1954 and Nicasio Reservoir in 1959 (Livingston, pers. Comm. in Niemi and Hall, 1996). These reservoirs further reduced the sediment contribution of Lagunitas Creek to the Tomales Bay marshland. Small deltas formed at the mouths of streams along both the east and west sides of Tomales Bay and waters filled the floodplain region of the lower reach of Olema Creek during the extensive flood that accompanied the 100-year storm of 1982 (Anima et al., 1988). Except for the effects of this storm, a study of aerial photos, sediment traps in Olema Creek, and a survey of drainage of the creek by Questa Engineering (1990), showed that there has been little change in sedimentation rates along this creek in the last few decades (Niemi and Hall, 1996). The rapid progradation at the southeastern end of Tomales Bay during the early years of settlement in the region was the direct result of introducing livestock and exotic plant species to the watershed, clearing land for agriculture, intensive logging in the latter half of the 19th century (Niemi and Hall, 1996). Analysis of maps by Niemi and Hall (1996) proved that the rate of marshland progradation in the southern parts of Tomales Bay slowed after 1954. After reaching a peak in the late 1800’s, the suspended sediment load introduced into Tomales Bay was significantly reduced when hills of the watershed became re-vegetated after logging ceased and several reservoirs were built along Lagunitas creek drainage. Niemi and Hall (1996) speculate that both the hydrological systems of the watershed remain partially destabilized and that the Tomales Bay tidal flats may continue to prograde due to ongoing development in the watershed. Storms such as the one that occurred in 1982 in West Marin also affect the watershed. Shoaling of approximately one foot was reported to have occurred in the vicinity of Inverness. The U. S. Geological Survey (USGS) reported an accumulation of sediment on the front of Lagunitas and Walker Creek deltas of approximately 10 million cubic feet after this flood (Anima et al., 1984).

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5.0 Effects of erosion and sedimentation on the watershed Soil erosion in the Tomales Bay watershed and subsequent sedimentation in the bay itself adversely affects water quality and the viability of marine habitats. Although some erosion occurs naturally, an increase in activities such as logging, agricultural practices, dams, construction, road building, and stream alterations since the mid 1800’s, has resulted in higher soil erosion rates, greater surface runoff, and less storage of water in the soil of the watershed. The effects of sedimentation are varied and can be significant to the survival of both the diversity of life and sustainable agriculture practices of the watershed. The primary effect of sedimentation in the watershed is the subsequent infilling of the Bay and accretion of its marshlands (Scholari, 1989). The reduction in the size of the bay has been seen, for example by the formation of deltas at the mouths of Lagunitas and Walker creeks. The loss of habitats including eelgrass beds and shoreline marshes such as at the mouth of tributary creeks (e.g., Olema Marsh and Livermore Marsh) has occurred due to their sensitivity to turbidity (California Coastal Conservancy, 1984). Salmonids (e.g., coho and steelhead) that spawn in the watershed are particularly vulnerable to sedimentation. When sediment deposits itself between beneficial gravel and cobble, it reduces the circulation of water, oxygen, and nutrients by forming a cemented surface (Prunuske Chatham, Inc., 1997; Prunuske Chatham, Inc., 2001). This deposition of sand and fine gravel reduces the volume of a pool as well as the spaces between rocks, thus diminishing both their rearing and winter refuge habitat (Kelley & Associates and Entrix, 1992). Road cuts, construction activities, and runoff from agricultural and ranching activities can produce run-off that clog tributary streams and wetlands, destroying habitats and interrupting invertebrates, fish and plant reproductive cycles. Siltation can also cause habitat loss for invertebrates, eelgrass, and other species along the shoreline and bay bottom and ultimately threatens the future of the entire bay and its ecosystem. Rapid sedimentation in the bay occurred over the past 130 years, peaking between 1930 and 1957, due to logging and agricultural practices. It is often impossible to distinguish between processes that are the result of human activities and natural processes. Many changes have occurred in the watershed following intensive land use practices in the late 1800’s and early 1900’s, as well as during big storms of the 1980’s and the early 1990’s (Daetwyler, 1966; UCCE, 1995; Prunuske Chatham, Inc., 2001). Over the past 130 years, sedimentation in the bay has averaged 1 kg•m-2.yr-1. This rate was amplified by poor agricultural practices and logging which produced rapid sediment delivery between 1930 and 1957 (6 kg•m-2.yr-1), however in recent years the rate of sedimentation has been near the long term average (Rooney, 1995) and recent land use practices have reduced the annual load. Although the rates of erosion and sedimentation are currently less than in the past, activities from the past still cause erosion which significantly affects the fragile ecosystems of this watershed. Tomales Bay Watershed Stewardship Plan: A Framework for Action 111

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6.0 Sedimentation in Walker and Lagunitas Creeks 6.1 Introduction The purpose of this overview is to summarize work that has been completed to analyze or address sediment and erosion issues within the Walker Creek and Lagunitas Creek subwatersheds and to identify where additional work is needed to implement the goals of the Watershed Council. Sediment transport in both streams affects Tomales Bay itself as well as local in-stream and riparian habitat. Although these impacts are closely intertwined, this section focuses on sediment transport issues within the watershed, while Sections 3-5 look at issues within the bay. Erosion and the subsequent movement of sediments through watercourses are natural processes that shape a stream and deliver nutrients and beneficial substrates to aquatic ecosystems. However, accelerated erosion directly or indirectly caused by human disturbance can overload channels with sediment. Too much sediment reduces capacity, fills wetlands and in-stream pools, and settles in the spaces between gravel and cobble to form a cemented, uniform surface on the stream bottom—poor habitat for young fish and aquatic insects. As channels form in the upper watersheds and deepen downstream, the water table is lowered, streams become entrenched, and riparian plants are perched above the water upon which they depend. Riparian wildlife species from frogs to songbirds to bats lose vital habitat. The key to effective sediment management lies in understanding what areas of the watershed are producing the most sediment, how it is moving through the system, and how it is affecting key resources. In both subwatersheds, pieces of this work have been done, but critical holes remain. 6.2 Walker Creek Watershed Topography in the 76-square mile Walker Creek watershed ranges from 1,500 feet to sea level, where the creek empties into Tomales Bay just south of its mouth. The northern tributaries, Keyes Creek and Chileno Creek, flow through wide valleys with gentle, grassy hills. The upper watershed is much more rugged with extensive areas of coast live oak forest. Soils, underlain by Franciscan formation sandstone and shale, are highly erodible (Kashiwagi, 1985). The watershed contains a 220-acre natural lake, Laguna Lake, at the top of Chileno Valley. Soulajule Reservoir, constructed in 1968 in Arroyo Sausal and enlarged in 1980, is managed by the Marin Municipal Water District (MMWD). Since European settlement, the land use has been almost exclusively agricultural. Cattle ranching is the predominant industry, along with a few sheep ranches and dairies. In recent years, vineyard development has spread into the eastern edge of the watershed. The only concentrated development in the watershed occurs in the small town of Tomales.

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6.2.1 History of Walker Creek Watershed Cattle came to the Walker Creek watershed with the first Mexican land grants. After the Gold Rush, Marin County became the primary producer of dairy products for the burgeoning San Francisco population. In 1866, Marin County produced three-fourths of California’s butter (Zumwalt, 1972). Even in 1880, the Sacramento Record-Union reported that Marin and Sonoma County pastures “afford constant, fresh and luxuriant grasses from January to September and October.” However, decades of continuous grazing combined with the plowing of watershed soils for crop production ultimately reduced the ability of the native perennial grasses to compete against introduced European annual grasses (Zumwalt, 1972; Edwards, 1992). Now, most west county ranchers begin feeding hay by late May or June, a telling indicator that the remaining perennials are too sparse to provide sufficient forage once the annuals have died. The change in watershed vegetation and land use instigated a dramatic period of erosion. The most frequently cited evidence of this erosion is the loss of Keys Creek as a navigable channel by the 1880s. From the 1850s into the early 1870s, potatoes were loaded onto shallow barges immediately downstream of the present Hwy. 1 (UCCE, 1995). Although much of this early erosion has healed, its effects linger on the landscape. The Soil Conservation Service (SCS) analyzed soils in large gully systems in the Stemple Creek watershed, Walker’s neighbor to the north, and determined that some were in their third cycle of active erosion (SCS, 1992). SCS theorized that these gullies began when the land was first cleared in the last half of the 19th century, and that they are reactivated with major storm events such as occurred in 1982 or 1986. Massive gully systems in similar soils and topography exist in the Chileno Creek and Keys Creek subdrainages (Prunuske Chatham, Inc., 2001). Compaction and the historic change in grassland composition are also blamed for increasing runoff rates in the upper watershed (Zumwalt, 1972; Kelley, 1976). As less rainfall is absorbed into disturbed, sparsely vegetated soils, more water flows on the soil surface and grassy swales are changed into eroding channels that continue to contribute bedload and suspended sediments to the stream system. W.W. Haible (1980) concluded that the upper reaches of Walker Creek had downcut 1 to 5 meters in the previous 60 years. Longtime Marin County rancher, Boyd Stewart, who lived at what is now the Walker Creek Ranch, illustrated this change with his memory of driving a horse and buggy easily across a section of the main channel that is now deeply incised (Stewart, 1995). Haible also found that the lower reaches of Walker Creek had aggraded 1 to 2 meters. Wehrhaftig and Wagner (1972) roughly calculated that the rate of erosion required from the Keyes Valley to have filled the lower channel in the period from 1852 to 1902 was 2,000 tons per square mile per year. Rooney and Smith (1999) state that “[m]uch of the floodplain contains an accumulation of >1 m of apparently recent stream sediments, for a total volume in excess of 107 m3 of sediments.” The lower valleys of Walker Creek appear to be storing a significant quantity of bedload. Tomales Bay Watershed Stewardship Plan: A Framework for Action 113

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Another major source of sediment in the Walker Creek watershed has been mercury mining. Several mines were operating in the watershed after World War II. The largest of these, the Gambonini mine, processed its own ore as well as ore from a neighboring mine in the Chileno Creek drainage. By the time the mine closed in 1970, 300,000 m3 of mine waste containing 300 tons of mercury had been piled onto 11 acres just upstream of the confluence of mainstem Walker and Salmon Creeks (Whyte and Ganguli, 2000; Kay, 2000). Buttes Gas & Oil, the last operator of the mine, built a tailings dam, contoured the fill, and seeded the site (Thurber, 1970). Following the severe 1981-82 winter, the stabilization measures failed. Whyte and Kirchner (2000) estimate that during the stormy winter of 1997-98, the mine site released 1.3 million kg (approximately 1,300 tons) of mercury-rich suspended sediments and an undetermined amount of bedload to downstream waters. This suggests that during the even more severe winter of 1981-82, millions of kilograms of sediment entered Walker Creek from the mine. The US Environmental Protection Act (USEPA), working with the San Francisco Bay Regional Water Quality Control Board (RWQCB), completed remediation of the site in 2000. Some of the bedload produced by the first flush of agriculture and more recent activities has made it to Tomales Bay. Daetwyler (1966) estimated that 3.3 million cubic yards of bedload has been deposited at the mouth of Walker Creek since 1861. Rooney and Smith (1999) used a GIS to compare four bathymetric surveys of Tomales Bay from 1861 to 1994. They concluded that sedimentation at the mouths of Walker and Lagunitas Creeks was greatest during the period from 1931 to 1957 and similar in the periods from 1861 to 1931 and 1957 to 1994. They assert that rapid land use changes in the first period produced the most erosion, but the sediment was delayed from reaching Tomales Bay by the storage capacity of the lower Walker Creek valleys, such as Keyes Creek. The recent sediment yield from the Gambonini mine as well as the Marin County Resource Conservation District (MCRCD) inventory of erosion sites (Prunuske Chatham, Inc., 2001) confirm that the Walker Creek watershed continues to produce significant quantities of sediment. 6.2.2 Summary of Recent Activities to Assess, Control and Monitor Sedimentation The only geomorphology assessment for Walker Creek was conducted in the mid 1970s by Haible (1980). Haible measured 13 sites along Walker Creek to determine changes in channel profile over time. He mapped the streambed, bedrock outcrops, a high terrace (carbon-dated in places as 5,000 years old), an inner terrace that was the floodplain around 1920, and the 1978 floodplain. He interviewed ranchers Boyd Stewart and James Marshall to determine changes at Walker Creek Ranch and at the Marshall Ranch near the mouth since about 1920. From this information, he concluded that in the previous 60 years, the stream had incised in the upper reaches, aggraded in the lower reaches, and extended its estuary. He discounted the impacts of tectonic uplift, subsidence or tilting, and concludes that changes in the “last 60 years are related to past and present watershed land use.” Several authors in the Tomales Bay Environmental Study (Corwan, 1972) addressed issues related to sedimentation in Walker Creek. Wehrhaftig and Wagner (1972) described the geological setting of Tomales Bay with a focus on slope stability and accelerated erosion on Tomales Bay Watershed Stewardship Plan: A Framework for Action 114

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the east side. Zumwalt (1972) chronicled changes in vegetation since European settlement and described the subsequent impacts on soil fertility and erodibility. He also made grazing management and other recommendations to improve range quality. Storm (1972) estimated runoff and sedimentation rates for the Tomales Bay watershed broken down by Lagunitas Creek, Walker Creek, and “bay margin watersheds.” He also wrote that “careful watershed management including the avoidance of overexploitation of natural range and grasslands should be a firm and unyielding policy for the Tomales Bay watershed.” MMWD commissioned several studies to assess the impact of raising Soulajule Dam on the Walker Creek fishery. In addition to recommending summer releases to sustain year round flow, Kelley (1976) found that streambed sedimentation contributed to the decline in salmonid populations. However, he identified “the accelerated runoff and intensification of the flash characteristics of floods” caused by overgrazing as the major culprit. After the big storms of the early 1980s, Bratovich (1984) and Rich (1989) identified embedded gravels and cobbles as a major factor in limiting salmonid populations. Rich also strongly recommended incorporating habitat and fishery monitoring into restoration activities. The MCRCD has offered outreach and assistance program to the landowners in the Walker Creek watershed since its founding in 1950. They commissioned an early hydrology study on the Lagunitas and Walker Creek watersheds (Nolte, 1965). The study estimated peak flood flows at 20 stations along Walker Creek and estimated annual average sediment yields to be 250 to 300 tons per square mile. In 1986, RCD received $1 million in funding as part of the California Coastal Conservancy’s Tomales Bay Enhancement Program to repair 14 large-scale erosion sites. At that time, over $6 million worth of erosion control projects were identified, not including landowner outreach, contract management, design, or permitting costs (Prunuske Chatham, Inc., 1986). MCRCD recently renewed its efforts in the watershed. The Walker Creek Watershed Enhancement Plan, focused around five landowner goals developed through an intensive community outreach effort, includes an erosion site inventory (Prunuske Chatham, Inc., 2001). Lands above Soulajule Reservoir and Laguna Lake were excluded because the survey focused on salmonid habitat. Of the remaining 51 square miles in the watershed, 21 landowners on 30 square miles granted permission to the MCRCD for survey access. Sites were located on a map, described, and given a repair priority based on estimated impacts to fisheries resources, erosion potential, activity, and access. Of the 196 sites inventoried, 30% rated a high priority. Over a third of the watershed landowners have already expressed their willingness to cooperate with MCRCD on enhancement projects. MCRCD has been awarded implementation funding from State Water Resources Control Board, the Department of Fish and Game, Coastal Conservancy, and others to implement projects to restore riparian habitat and reduce erosion. Work is currently underway. Additional erosion control work has been performed by private landowners, the Marin Motorcycle Club on the Gambonini Ranch, and the Marin County Office of Education on the Walker Creek Ranch. The Natural Resource Conservation Service (NRCS) continues to provide technical assistance and cost-share programs that encourage landowners to Tomales Bay Watershed Stewardship Plan: A Framework for Action 115

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implement best management practices. UCCE offers ongoing range management education and advice to Walker Creek watershed ranchers. UCCE staff members are also working closely with the Tomales Bay Agriculture Group (TBAG), which includes several Walker Creek watershed landowners, to monitor water quality on participating dairies and implement measures to reduce targeted pollutants. The San Francisco Bay Regional Water Quality Control Board (RWQCB) is continuing to monitor mercury movement through sediments and bioaccumulation in Walker Creek and Tomales Bay. 6.3 Lagunitas Creek Watershed At 103 square miles, the Lagunitas Creek watershed is the largest drainage to Tomales Bay. It differs greatly from Walker Creek in many ways. First, rainfall in the upper watershed averages 50 inches per year, compared to 25 in Chileno Valley. Halleck Creek, Nicasio Creek, San Geronimo Creek, and mainstem Lagunitas through Samuel Taylor State Park have areas of dense redwood growth and cool water year round. Except for a few open areas, most of Lagunitas Creek downstream of the state park is thickly forested with willows and alders. Over half of the watershed is in public ownership with a corresponding increase in opportunities for consistent, comprehensive management. Ranching, much of it on land leased from the National Park Service (NPS), continues in the Olema and Nicasio Valleys and in lower Lagunitas. One cattle ranch remains in San Geronimo Valley. The Lagunitas Creek watershed also contains many small communities —Woodacre, San Geronimo, Forest Knolls, and Lagunitas in San Geronimo Valley, Nicasio, Olema, and Point Reyes Station at the mouth. The upper part of the watershed is owned and managed by MMWD for water supply to east Marin County. MMWD has five reservoirs in the watershed—four on mainstem Lagunitas Creek and Nicasio Reservoir on Nicasio Creek. The Lagunitas Creek watershed has been the focus of salmonid restoration efforts for over twenty years. Coho salmon populations have rebounded from tens of fish returning in the early 1980s to an average of 500 adults the past few years with up to 800 returning in some years (Andrews, 2002). Last year they were joined by a few Chinook salmon and a sturdy run of steelhead trout. Olema Creek at the southwestern edge of the watershed flows in nearly a straight line through a rift valley along the San Andreas fault zone. West of the fault, soils are derived from Tertiary sedimentary rock; east of the fault zone, soils are formed from Franciscan formation (Kashiwagi, 1985; Niemi and Hall, 1996). The lower reaches of Olema Creek flow through a deep alluvial fan. Hecht (1979) notes that the Franciscan greenstones and associated metavolcanic rocks found in the reaches of Lagunitas Creek with the best salmonid rearing habitat are “unusually reliable sources of cool, good quality water.” Soils on moderate to steep slopes on both sides of the fault zone are highly erodible (Kashiwagi, 1985).

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6.3.1 History of Lagunitas Creek Watershed Lagunitas Creek watershed has a much more varied and dramatic land use history than Walker Creek. Commercial logging began in the upper Lagunitas Creek watershed in the 1860s and moved downstream until nearly all of the old growth Douglas fir and redwood trees were harvested (UCCE, 1995). Logging continued in the Olema Creek Watershed until 1962. Major fires have burned portions of the watershed several times. Samuel P. Taylor built the west’s first paper mill on mainstem Lagunitas Creek near Devils Gulch in 1856. It ran 24 hours a day until it closed in 1893. Dairy farming, beef and sheep production, and potato growing dominated the more open landscapes of the lower watershed and San Geronimo, Nicasio and Olema Valleys. Gravel and sand were mined from the streambed at the confluence of Lagunitas and Nicasio Creeks until a short time after Nicasio Dam was constructed in 1960. Ranchers regularly harvested small amounts of streambed gravel to maintain ranch roads through the 1980s. The first reservoir, Lagunitas Lake, was built in 1872 and followed by Alpine Lake in 1919, and then by Bon Tempe in 1949. Peters Dam, built in 1954 to form Kent Lake, was raised 45 feet in 1982, nearly doubling reservoir capacity from 16,600 acre feet to 33,000 acre feet. In addition to blocking anadromous fish passage to miles of spawning and rearing habitat, the impoundments have altered streamflows and stopped bedload transport from the upper reaches of the watershed. In the early 1920s, Olema Creek between the town of Olema and its confluence with Lagunitas Creek was straightened into the 3-kilometer long “Olema Canal.” The canal drained the surrounding land for agricultural production. Niemi and Hall (1996) located a nickpoint, an abrupt change in the gradient of the stream bottom, 4.3 kilometers upstream from the confluence with Lagunitas Creek. They suggest that this nickpoint began with the canal construction and has since migrated upstream. As lower Olema Creek deepened, lower Lagunitas Creek filled in. Rapid deforestation, agricultural development, extensive road construction, and the completion of the railroad in the 1870s contributed to significant erosion and subsequent sediment accumulation at the head of Tomales Bay. Construction of levees and seasonal dams near the mouth of Lagunitas Creek artificially regulated tidal circulation and “promoted sedimentation at the mouths of the tidal channels (Niemi and Hall, 1996). Niemi and Hall compared maps and sketches of the lower Tomales Bay area from 1858 to 1954 and found that the greatest deposition occurred between 1860 and 1918 when the tidal marsh prograded more than a kilometer to the northwest. Rooney and Smith (1999), in their comparison of bathymetric surveys from 1861 to 1994, showed that, although overall sedimentation rates for Tomales Bay were highest between 1931 and 1937, accumulation of sediment at the Lagunitas Creek delta was greatest from 1861 to 1931. Even though sedimentation rates have slowed, Niemi and Hall predicted that the lower Tomales Bay tidal flats will continue to expand faster than pre-1860s rates.

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The January 1982 storm caused significant recent changes to the Lagunitas Creek delta. Shoaling extended so far into Tomales Bay that boats can no longer reach the Inverness Yacht Club at low tide. USGS estimated that 108 cubic yards of soil were deposited on the Walker and Lagunitas Creek deltas following that storm (Anima et.al., 1984). 6.3.2 Summary of Recent Activities to Assess, Control and Monitor Sedimentation 6.3.2.1 Mainstem Lagunitas Creek The raising of Peters Dam initiated a period of intensive analysis of the geomorphology and aquatic habitat of Lagunitas Creek. Local residents and public agencies were concerned that the expansion could severely threaten the fragile salmon runs. In 1979, MMWD retained D.W. Kelley and Associates to assess salmonid rearing habitat and fish populations in order to evaluate proposed flow releases from Kent Lake. They found a consistent exponential decline in juvenile steelhead populations as the amount of sand embedded in the cobble increased (Kelly and Dettman, 1980). Kelley and Bratovich (1988) concluded that if “sedimentation can be reduced, the rearing capacity of Lagunitas Creek will increase.” A later review of the Kelley studies reiterated the need for sediment reduction in rearing habitat (Kelley and Entrix, Inc., 1992). “Besides enhancing instream flows, the most important thing to enhance Lagunitas Creek and restore its coho and steelhead stocks as near as possible to levels that existed many years ago, is to reduce sediment in every manner available.” (Kelley and Entrix, Inc. 1992). Geomorphologist Barry Hecht also began a series of investigations in 1979 for MMWD in order to develop a sediment management plan that would support a viable salmonid fishery (Hecht, 1992). Hecht identified coarse sand and fine gravel, 1 to 8 mm size range, as the impairing sediment for rearing habitat. Through mineralogical tracings, measurements of sediment transport, and observation, he concluded that most of the sediment accumulated on the bed of Lagunitas Creek originated in San Geronimo Valley. Nicasio Valley has contributed most of the bedload below Nicasio Creek (Hecht, 1983). Hecht recommended that reducing the coarse sediment delivery from San Geronimo Creek by 10 to 20% “would likely offset the diminished flushing capacity” caused by the raising of Peters Dam (Hecht and Woyshner, 1988). Surveys of erosion sites along San Geronimo Creek itself and throughout the watershed were conducted (Chatham, 1987; Prunuske Chatham, Inc., 1990.) In 1994, MMWD began a sediment management program to reduce the annual fine sediment load from San Geronimo Creek by 600 tons or approximately 15% through a combination of source control and small sediment traps. A monitoring program was also developed to measure the impact of the sediment control projects on bed conditions (Hecht, 1992). MMWD contracted with Marin County RCD to implement the sediment control program and conduct ten years of monitoring. The monitoring program, now in its seventh year, includes an evaluation of general streambed conditions and measurements of the channel bed elevation, bed surface composition, and bed core composition. Data has been collected but has not been analyzed.

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After years of studies and sometimes fierce public debate over the relative importance of sedimentation versus streamflow on in-stream habitat, the issue of water releases was finally resolved through State Water Board Order WR 95-17. The Order set in-stream flow and temperature requirements and mandated a more comprehensive sediment management plan. The Order also requires MMWD to monitor for coho salmon, steelhead and freshwater shrimp populations in Lagunitas Creek (SWRCB, 1995). The Lagunitas Creek Sediment and Riparian Management Plan (Prunuske Chatham, Inc., 1997) identified additional measures to reduce the delivery of fine gravel and sand to Lagunitas Creek and to increase larger gravel and cobble between Peters Dam and Shafter Bridge. The measures were based on another erosion site survey of lands between Shafter Bridge and Tocaloma. MMWD is continuing to prioritize and undertake projects to improve bed conditions in Lagunitas Creek. Recently, they commissioned a survey to assess the sources and amount of sediment coming off their watershed road system. Point Reyes National Seashore (PRNS) began a water quality program on National Park watershed lands in 1999. PRNS is testing for many parameters, including total suspended sediments (TSS), at 14 sites on Olema Creek and 3 sites in the remainder of the Lagunitas Creek watershed (Point Reyes National Seashore, 2001). PRNS has recently focused on enhancing aquatic habitat in their lands through riparian protection, removal or modification of barriers to fish passage, range management, and erosion control. MCRCD completed an earlier round of erosion control projects in the Lagunitas Creek watershed from 1983 to 1987. Project locations ranged from the very top of the watershed, where channel downcutting was stabilized at the Flanders Ranch in Woodacre, to Point Reyes Station where a massive gully on the Genazzi Ranch was repaired (Prunuske Chatham, 1988). An important part of the Marin County RCD program was to coordinate the maintenance of unsurfaced ranch and fire roads by the Marin County Fire Department, MMWD, Samuel P. Taylor State Park, and local ranchers. Trout Unlimited organized their first volunteer project in the Lagunitas Creek watershed at the Giacomini Dam in the 1970’s. Since then, they have orchestrated many work days in which hundreds of volunteers have strung fence, built checkdams and fish ladders, and passed gravel through bucket brigades to the scoured reach below Peters Dam. Trout Unlimited also maintained hatch boxes in the mid 1980s on small tributary streams where eggs stripped from wild Lagunitas coho salmon were protected from predators and unstable bed conditions. The Salmon Protection and Watershed Group (SPAWN) was recently awarded grant funding for water quality monitoring, community outreach, and restoration projects including sediment control. 6.3.2.2 Olema Creek Within the Olema Valley major land use shifts, alterations to the channel, and climatic events are connected to the geomorphic character of the existing stream channel and habitat condition (PRNS, 2001). PRNS commissioned a three-year study to identify sediment sources in Olema Creek, compare current and historic rates of erosion and sedimentation, and Tomales Bay Watershed Stewardship Plan: A Framework for Action 119

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develop watershed management recommendations (Questa, 1990). The study found that the upland watershed was in good condition with little change over the previous 40 years. Questa estimated the total sediment yield from the watershed to be 1790 tons per square mile with 62 percent originating from channel erosion along Olema Creek. They recommended, however, that erosion control efforts focus on gullies and other surface erosion problems because streambank stabilization in the fault zone of mainstem Olema Creek would be prohibitively expensive and diminish the natural character of the creek. PRNS is also undertaking water quality monitoring and habitat enhancement projects in the Olema Creek watershed. Fisheries and water quality assessment of Olema Creek watershed during 1999-2001 indicate that the effects of past land-use practices (logging, agriculture, and grazing) have altered the condition of the watershed, effecting its ability to support fisheries at their historic levels (PRNS, 2001). Although landuse activities have been greatly reduced and upgraded in many ways, present landuse continues to influence water quality conditions within the watershed. Loss of native perennial vegetation, soil compaction and loss, hillside trailing, gullying, and incision of swales and meadows have changed the runoff patterns and reduced the capacity of the watershed to attenuate pollutant loading and surface runoff (PRNS, 2001). Major storm events during the last three decades, in combination with two droughts and two El Nino events, resulted in catastrophic debris flows and delivery of sediment to the Olema Creek channel. In some areas major sediment deposition resulting from the mobilization of materials deposited in the channels in1982 and 1983 is still visible (PRNS, 2001). According to the 1999-2001 PRNS monitoring results, seven to nine inches of cumulative rainfall are required to initiate significant response and connectivity of the entire Olema Creek system. This event is considered the first flush water quality event, delivering accumulated sediment and pollutants from land-based source areas, and often coincides with the initial upstream migration by coho salmon. 7.0 Preliminary geomorphologic assessment recommendations These assessment recommendations are intended to support prioritization of future habitat enhancement and water quality improvement projects in the bay and watershed. These recommendations have not yet been prioritized by the Tomales Bay Watershed Council, and are thus intended to provide a starting point for future discussion and planning activities. •

Analyze the sediment transport functions in the Lagunitas Creek system with respect to their impact on instream habitat and on sediment delivery to Tomales Bay. In Lagunitas Creek, such analysis will increase understanding of how the sediment transport function influences critical habitat features such as pool riffle complexes and bed material composition. This information is critical to the design of effective restoration projects. Lead: MMWD or Marin County RCD Partners: SPAWN, Trout Unlimited, PRNS, RWQCB, Marin County, Tomales Bay Watershed Council, Tomales Bay Association and others

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Schedule: Work has been initiated, but an additional 2-3 years would be necessary to collect good winter data. Cost estimate: $200,000 to complete assessment on areas beyond scope of current Proposition 13 grant (“Lagunitas Creek Watershed Improvement Program”) •

Inventory and prioritize sediment sources in upper Devil’s Gulch and mainstem Lagunitas Creek below Tocaloma. Include a road assessment on the areas of the watershed not covered by the current MMWD effort. Lead: Marin County RCD Partners: MMWD, PRNS, Tomales Bay Watershed Council, Marin County and others. 6 months. Schedule: 2 years Cost estimate: $75,000

•

Conduct a fluvial geomorphic analysis of the Walker Creek stream system. The analysis will provide a scientific basis for selection, design, implementation and monitoring of future fisheries habitat enhancement and sediment reduction projects. Coordinated with RWQCB monitoring efforts, it will also provide critical information on the movement of mercury-laden sediments through Walker Creek to Tomales Bay. Lead: Marin County RCD Partners: Tomales Bay Watershed Council, RWQCB, local ranchers. Schedule: 2 years Cost estimate: $120,000

•

Develop a, comprehensive, hydrodynamic watershed-wide sediment budget and monitoring program to assess the impacts of enhancement measures both within the watershed and Tomales Bay that includes: 1) water column, 2) bedload, 3) upland sources and 4) habitat monitoring. Evaluate the MMWD sediment monitoring program in Lagunitas Creek and determine what it can contribute to the larger program. Analyze the data collected to date. Lead: Tomales Bay Watershed Council and USGS Partners: MMWD, Marin RCD, RWQCB, PRNS and others

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Literature cited Andrews, Gregory, 2002. Marin Municipal Watershed Council. Personal communication. Anima, R, J.L. Bick, and H.E. Clifton. 1988. Sedimentologic consequences of the storm in Tomales Bay. In Landslides, floods, and marine effects of the storm of January 3-5, 1982 in the San Francisco Bay region, California. U.S. Geological Survey Professional Paper 1434. Bratovich, Paul M. 1984. Walker Creek Survey. Memo to Don W. Kelley, D.W. Kelley and Associates, October 12, 1984. California Coastal Conservancy. 1984. A Program for Restoring the Environment of Tomales Bay. California Coastal Conservancy, Oakland, California. 28 pgs. Chatham, S. 1987. Interim Report. San Geronimo streambank erosion. Prepared for Marin Municipal Water District. Corwin, Ruthann (ed.). 1972. Tomales Bay Environmental Study. Washington D.C: The Conservation Foundation. Daetwyler, C.C. 1966. Marine Geology of Tomales Bay, Central California. Scripps Institution of Oceanography: research Report No. 6. 169 pp. Edwards, S.W. 1992. Observations on the prehistory and ecology of grazing in California. Fremontia. 20(1): 3-11. Evens, J.G. 1993. The Natural History of the Point Reyes Peninsula. Revised Edition. Point Reyes National Seashore Association. 224 pp. Galloway, A. J. 1977. Geology of the Point Reyes Peninsula, Marin County, California. California Division of Mines and Geology Bulletin 202. Sacramento, CA. Haible, W.W. 1980. Holocene profile changes along a California coastal stream. Earth Surface Processes. 5: 249-264. Hecht, B. 1983. Substrate enhancement/sediment management study, Lagunitas Creek, Marin County-Phase IIIb: Sediment transport and bed conditions, 1979-1982: H. Esmaili & Associates consulting report prepared for the Marin Municipal Water District, 173 p. Hecht, B. 1992. Sediment overview report: development of an initial sediment-management plan for Lagunitas Creek, Marin County, California. Prepared for Marin Municipal Water District. Hecht, B. and M.R. Woyshner. 1988. Status summary report. Substrate enhancement /sediment management plan, Lagunitas Creek. Prepared for Marin Municipal Water District. Kashiwagi, J.H. 1985. Soil Survey of Marin County. U.S. Department of Agriculture, Soil Conservation Service. Kay, J. 2000. Tainted Tomales. Article in the San Francisco Examiner. 1/9/00. Kelley, D.W. 1976. The possibility of restoring salmon and steelhead runs in Walker Creek, Marin County. Prepared for Marin Municipal Water District. Kelley, D.W. and D.H. Dettman, 1980. Relationships between streamflow, rearing habitat, substrate conditions, and juvenile salmonid populations in Lagunitas Creek, Marin County. Prepared for Marin Municipal Water District. Kelley. D.W. and P.M. Bratovich, 1988. Investigations of salmon and steelhead in Lagunitas Creek, Marin County, California. Vol. 1. Migration, spawning, embryo incubation and emergence, juvenile rearing, emigration. Prepared for Marin Municipal Water District.

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Kelley, D., & Associates, and Entrix Inc. 1992. Habitat recommendations for Lagunitas Creek, California. Report prepared for the Marin Municipal Water District, Corte Madera, California. Plant, J.N. 1995. Effects of land use change on Tomales Bay, California: new ideas from old tracers (microfiche). Master’s Thesis. University of Hawaii. Scholari, J. 1989. Olema Marsh - a study site for the effects of marsh accretion on Salix (willow) species. Report to the Audubon Canyon Ranch and the University of Santa Cruz. 15 p. Niemi, T.M, N.T. Hall, 1996. Historical changes in the tidal marsh of Tomales Bay and Olema Creek, Marin County, California. Journal of Coastal Research. 12(1): 90-102. Nolte, G.S. 1965. Master drainage and sediment control plan. Lagunitas and Walker Creek watersheds. Prepared for Marin County Resource Conservation District. Point Reyes National Seashore, National Park Service (PRNS). 2001. Water quality monitoring report, May 1999-May 2001. Prunuske Chatham, Inc. 1988. Final report of the Lagunitas watershed erosion control program. Prepared for Marin County Resource Conservation District. Prunuske Chatham, Inc. 1986. Report of findings and recommendations of an inventory of erosion programs in the watershed. Walker Creek Watershed Restoration Program. Prepared for Marin County Resource Conservation District. Prunuske Chatham, Inc. 1990. San Geronimo Creek watershed bedload reduction opportunities. Prepared for Marin Municipal Water District. Prunuske Chatham, Inc. 1997. Lagunitas Creek Final Sediment and Riparian Management Plan. Prepared for Marin Municipal Water District in compliance with California State Water Resources Control Board Order WR95-17. Prunuske Chatham Inc., Occidental, CA. 132 pgs. + appendices A-K. Prunuske Chatham, Inc. 2001. Walker Creek Watershed Enhancement Plan. Prunuske Chatham, Inc., Occidental , California. 55 pgs. Prepared for Marin County Resource Conservation District. Questa Engineering Corp. 1990. Olema Creek Erosion and Sedimentation Study. prepared for National Park Service 75 pp. plus appendices. Rich, A.A. 1989. Fishery Resources Habitat Surveys in Walker Creek, Marin County. Prepared for Marin County Resource Conservation District 22 pp. plus appendices. Rooney, J.J. 1995. Determination of sedimentation rates in Tomales Bay, California using a geographic information system. M.S.Thesis, University of Hawaii. Rooney, J.J. and S.V. Smith. Watershed landuse and bay sedimentation. 1999. Journal of Coastal Research. 15(2): 478-485. Soil Conservation Service. 1992. Erosion and sediment study: Stemple Creek watershed. In Stemple Creek/Estero de San Antonio watershed enhancement plan. Prepared for Marin County Resource Conservation District and Southern Sonoma County Resource Conservation District. State Water Resources Control Board (SWRCB). 1995. Order: 95-17. Lagunitas Creek. Stewart, Boyd. 1995. Personal Communication. Storm, D. R. 1972. Hydrology and water quality aspects of the Tomales Bay Study, in Tomales Bay Environmental Study (R. Corwin, ed.), pp. 84-101. Conservation Foundation, Washington, D.C. Thurber, S. 1970. Healing a mining operation’s scars. Article in San Francisco Chronicle. Tomales Bay Watershed Stewardship Plan: A Framework for Action 123

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11/26/70. University of California Cooperative Extension. 1995. The Marin Coastal Watershed Enhancement project. University of California Cooperative Extension. Novato, California. 83 pgs. Wehrhaftig, C. and J.R. Wagner. 1972. The geologic setting of Tomales Bay. In Tomales Bay Study: A Compendium of Reports. Prepared for the Conservation Foundation. Whyte, D. C. and J. W. Kirchner. 2000. Assessing water quality impacts and cleanup effectiveness in streams dominated by episodic mercury discharges. In The Science of the Total Environment 260: 1-9. Whyte, D.C. and P.M. Ganguli. 2000. The impact of mercury mining on Tomales Bay biota. EPA mercury conference. University of California Cooperative Extension (UCCE). 1995. Final report of the Marin Coastal Watershed Enhancement Project. Zumwalt, Clerin W. 1972. “Consideration of vegetation and soils on the Tomales Bay Watershed” In Tomales Bay Environmental Study, (Ed.) Corwin, Ruthann, Washington D.C: The Conservation Foundation.

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APPENDIX C. Glossary of Common Ecological and Watershed Related Terms The following references were consulted in compiling this glossary: 1. King, Neysa. 2000. A Citizen’s Guide to Watershed Conservation. Unpublished M.S. Thesis. University of Montana, Missoula. 2. EPA glossary of terms http://www.epa.gov 3. FishBase http://www.fishbase.org A adaptive management: A management strategy that acknowledges the inherent uncertainty that exists in managing natural ecosystems given their interconnected nature and natural complexity. Adaptive watershed management is based on making management decisions that use the best available scientific information and technical advice, and monitoring both intended and unintended effects implemented project. Through careful monitoring, adaptive management plans and actions are modified when an undesirable impact is found. Adaptive management espouses proceeding with caution, and when choosing between different restoration alternatives, prefers actions that are reversible over those that cannot be undone. anadromous fish: Fish that leave freshwater and migrate to the ocean to mature then return to freshwater to spawn. algal/algae bloom: enrichment.

Rapid growth of algae in a waterbody, commonly stimulated by nutrient

aquiculture: The process of farming aquatic organisms aquifer: A geological formation or structure that stores and/or transmits underground water. B bank stabilization: Implementing measures along a streambank to prevent or reduce bank erosion. base flow: Portion of stream discharge derived from such natural storage sources as groundwater, large lakes, and swamps but does not include direct runoff and other forms of surface water. basin: See river basin. bedrock: A general term for solid rock that lies beneath soil, loose sediments, or other unconsolidated material. beneficial uses: The use of water for human benefit consistent with the protection of aquatic ecosystems, with the ultimate goal of achieving the highest water quality while providing maximum benefit to the people of the state. Aquatic ecosystems and underground aquifers provide many different benefits to the people of the state, and the Regional Water Quality Control Board is charged with protecting these benefits. Beneficial uses of water include but are not limited to fish and wildlife habitat and/or passage, agriculture, mariculture, domestic, estuarine and marine habitats, areas of special biological significance, preservation of rare and endangered species, irrigation, fishing, municipal supply, and recreational uses.

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best management practices: Methods adopted by resource users to control nonpoint source pollution or maintain the health and integrity of the watershed. benthic: Bottom dwelling or substrate-oriented; at or in the bottom of a stream or lake. bioengineering: Combining structural, biological, and ecological concepts to construct living structures for erosion, sediment, or flood control. biological diversity (biodiversity): Variety and variability among living organisms and the ecological complexes in which they occur; encompasses different ecosystems, species, and gene forms. biological integrity: The ability of an ecosystem to support and maintain a balanced, integrated, adaptive community of organisms having a species composition, diversity, and functional organization comparable to that of natural habitat of the region; a system’s ability to generate and maintain adaptive biotic elements through natural evolutionary processes. biological oxygen demand (BOD): Amount of dissolved oxygen required by decomposition of organic matter in water. biomass: Summed mass or weight of individuals in one or more species, usually related to a defined area or volume; a measure of the abundance of a life form. braided stream: Stream that forms an interlacing network of branching and recombining channels separated by branch islands or channel bars. C carrying capacity: Maximum number of organisms that an be sustained in a habitat over the long term. Usually refers to a particular species, but can be applied to several species with similar resource needs. channelization: Artificially straightening the meanders of a river; often accompanied by placing riprap or concrete along banks to stabilize the system. check dams: Series of small dams placed in gullies or small streams in an effort to reduce the erosive power of water. Clean Water Act: Passed in 1972, this federal act directs the Environmental Protection Agency to set nationwide criteria and policies to restore and protect water quality. confluence: Joining. Commonly used in reference to where two rivers or streams join into one. consensus: A process whereby every decision must be approved by all participating persons, and every person maintains the power to veto the final decision of the group. conservation: Sustainable use of ecosystems and their associated resources and services; the continuing protection and management of ecosystems in accordance with principles that prioritize their optimum long-term ecological, economic and social benefits.

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cumulative impacts: The combined effect on an ecosystem’s integrity of all of the land and water uses within a watershed or basin. These impacts can have a synergistic impact that is greater than simply adding them together. D designated use: Designated uses are human and ecological water uses that are officially recognized and protected under the Clean Water Act. (See definition of beneficial uses) discharge: An outflow of water from a stream, groundwater system, pipe or watershed. disturbance regime: Characteristics (timing, duration, and intensity) of natural (occasionally artificial) disruptions such as floods, wildfires, volcanoes, etc. Natural disturbance regime is the regime that occurred before human-caused disturbance became significant. diversity: The richness and variety of species, habitats, or ecosystems. drainage basin: The entire land area from which precipitation runs off into streams, rivers, lakes, and reservoirs. Also called a "watershed." E ecological restoration: Involves replacing lost or damaged biological elements (populations, species) and reestablishing ecological processes (dispersal, succession) to more natural levels. ecosystem: A biological community together with the chemical and physical environment with which it interacts. ecosystem management: Management that integrates ecological relationships with sociopolitical values toward the general goal of protecting or restoring long-term ecosystem integrity. effluent: A waste liquid discharged from a manufacturing or treatment process into the environment. endangered species: A technical term used to classify a species that is in danger of extinction throughout all or a significant portion of its range and is thus protected by the U.S. Endangered Species Act and/or additional state regulations. enhancement: To improve stream or watershed quality. Enhancement activities include restoring large woody debris to a stream to improve fish habitat, revegetating riparian vegetation, decreasing point source pollution caused by logging activities to improve water quality, etc. ephemeral: Streams and creeks that flow only during periods of intense rainfall or high groundwater. See perennial and intermittent. erosion: The wearing down or washing away of the soil and land surface by the action of water, wind or ice. estuary: A partially closed body of water where freshwater rivers and streams flow into the

ocean, mixing with the seawater

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eutrophication: A process in which a waterbody becomes more nutrient-enriched, aquatic life increases, and dissolved oxygen and other water chemistry parameters fluctuate more widely, reducing the suitability of the habitat for some life forms. F floodplain: The relatively flat area found along a stream through which the stream flows periodically when it overflows its banks. Floodplains slow and absorb high floodwaters, and depend on the sediment deposited during flood events for normal ecosystem processes. G goal: General statements that express the broad focus of the entire planning and conservation effort. A goal of many watershed conservation efforts is to restore wildlife habitat populations and beneficial uses. Compare to objective. groundwater: Water that flows beneath the ground surface that supplies springs and wells. H habitat: The environment where a plant or animal grows or lives. habitat modification: Activities that destroy or degrade the physical integrity of an aquatic or terrestrial ecosystem. In an aquatic system, habitat modification results from changes in streamflows, lake levels, and water temperature. headwaters: Upper tributaries of a river or stream; the water source from which the stream or river originates. human waste: Human excretions and septic material. hydrologic cycle: The constant circulation of water from the sea, through the atmosphere, to the land, and back to the sea by overland, subsurface, and atmospheric routes. I impaired waters: Waters that do not fully support their designated uses. infiltration: Water that seeps into the soils. instream flow: Water in streams or rivers that is used for nonconsumptive purposes such as the preservation and enhancement of fish, wildlife, recreation, navigation, and power generation. intermittent stream: A stream that has flowing water only part of the year. invasive species: Any plants, animals, or other species that have been successfully introduced and has caused damage to an ecosystem beyond its historic range, both through intentional and nonintentional human activities. Also called "alien species," "nonnative species," "aquatic nuisance species," "introduced species," and exotic organisms.” invertebrates: Invertebrates are animals without backbones, and include terrestrial insects in addition to stream and bottom dwellers that include: clams, worms, snails, crabs, shrimp, beetles, aquatic insects, jellyfish, etc.

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irrigation: The controlled application of water to cropland, hayland, and/or pasture to supplement water supplied by nature. M mariculture: The process of farming aquatic organisms in a marine environment. mainstem: A wider, deeper stream or river channel that is joined by smaller, headwater tributaries. meander: The curves in a stream as it flows through its floodplain. mitigation: An action designed to lessen or reduce adverse impacts; frequently used in the context of minimizing harm to the environment. monitoring: A method of evaluating the condition and change of a stream or specific part of an ecosystem. Monitoring systems use physical, chemical and biological measurements to track the condition and changes in a watershed or stream ecosystem. N natural flow: The flow of a stream as it would be if unaltered by any upstream activities, including: diversion, storage, import, export, or changes caused by development in floodplains, etc. nonconsumptive use: The use of a resource that does not decrease the supply, flow or level (e.g. fish spawning, swimming, bird watching, hiking, etc.). nonpoint source pollution: Contaminants that flow with rain runoff from the land into the sea

or through the atmosphere and are deposited onto the land or water, and eventually into the ocean. Also called polluted run-off or seepage. nutrients: Elements or compounds essential to life, including carbon, oxygen, nitrogen, phosphorus, and many others. O objective: Specific, measurable actions developed and implemented to support each aspect of a goal. Compare to goal. P pathogen: Disease-causing microorganism, virus, bacterium or fungi. perennial stream: A stream that flows year-round. plan: A compilation of goals and objectives, policy statements, and implementation strategies for guiding actions or decisions to meet perceived needs or to avoid problems. point source pollution: Pollutants discharged from an identifiable point including pipes, ditches, channels and sewers. All point sources of pollution require a discharge permit. precipitation: Water falling, in a liquid or solid state, from the atmosphere to a land or water surface.

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R reach: Any designated part of a stream along its length. recharge: The addition of water to rivers or aquifers which tends to raise or maintain the water table. rehabilitation: To restore a portion of a watershed to good health. Rehabilitation projects include replanting riparian vegetation in areas where clearing has occurred; restoring the physical structure to a stream to improve a fishery; etc. remediation: To correct or remove causes of degradation; to put right. Watershed remediation may include removing dams, culverts, restoring a river’s access to its floodplain, etc. restoration: A holistic process aimed at reestablishing ecosystem structure and function (ecosystem parts and processes). riparian vegetation: The plant community adjacent to a stream or lake that requires shallow groundwater. Common riparian vegetation includes sedges, willows, alders and cottonwoods. Riparian vegetation is important to the aquatic community as it provides organic material, shade and cover while stabilizing streambanks and serving as a buffer between landuses within the watershed and the waterbody itself. runoff: See surface runoff. S salmonid: Fish of the family Salmonidae, including: salmon, trout, chars, whitefish, etc. shellfish: Any aquatic organism with a shell. e.g. crustaceans (i.e. lobster, crab and shrimp) and mollusks (i.e. oysters, mussels, and clams). Shellfish Protection Act: Passed by the California Legislature in 1993, requires the Regional Water Quality Control Board (RWQCB) to form Technical Advisory Committees (TACs) in areas where commercial shellfish are determined to be threatened. sediment: Fine soil-like particles produced by the weathering of soil and rock. Suspended sediment is that which is suspended in the water column of a stream or lake. sedimentation: The building up of sediments in a body of water. sewer: A system of underground pipes that collect and deliver wastewater to treatment facilities. sewage treatment plant: A facility designed to receive the wastewater from domestic sources and to remove materials that damage water quality and threaten public health and safety when discharged into receiving streams or bodies of water. stormwater: Storm water runoff, snow melt runoff, and surface runoff and drainage. surface runoff: Precipitation (rain or snow) that reaches the ground and remains on the surface, until it runs off into streams and bays as overland flow. Compare to infiltration.

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surface water: Water on or above the surface of the land, including lakes, rivers, streams, ponds, flood water, and runoff. T terrestrial: Living or growing on land. threatened species: A classification referring to a species that is likely to become endangered within the foreseeable future, throughout all or a significant portion of its range, as defined by the federal Endangered Species Act. topography: The three-dimensional shape of the land surface. Total Maximum Daily Load (TMDL): A watershed-wide pollution budget and associated clean up plan. TMDL refers to the maximum amount of pollutant or disturbance that a waterbody can assimilate without unacceptable change (impairment). TMDLs are required for waters on a state’s list of impaired waterbodies. tributary: A smaller feeder stream that empties into a larger mainstem stream. W waste: See human waste and non-human waste refers to animal excretions. waterbody: A stream, river, lake, wetland or ocean. water budget: An accounting of the inflows and outflows of water to and from a system. water right: A legal right to use a specified amount of water for beneficial purposes (under the doctrine of prior appropriation which holds in the western US). water quality criteria: Numeric or narrative descriptions of the conditions considered necessary to protect a desired water use as required under the Clean Water Act. See designated use. watershed: The entire surface drainage area that contributes water to a water body (river, lake or wetland). Also called a catchment area or a drainage basin. watershed integrity: the capability of a watershed to support a healthy, viable biological community and the hydrologic, evolutionary and habitat requirements a watershed ecosystem depends upon. Tangible measures of watershed integrity include: water yield and quality; species composition, diversity, and abundance; wildlife use; and genetic diversity. weed: Plants that threaten the welfare of an ecosystem or human commodity by competing with other plants. wetland: A landform characterized by the presence of water, saturated soils, and water-loving vegetation.

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Appendix D. Summary Responses to Public Comments This appendix has been included to better understand the issues raised by the community during the public outreach period as well as a way for the community to better understand how the Council is currently, or will in the future, address concerns and suggestions that have been raised during recent months. All of the comments that were received during the public review process are available on the Council’s website http://www.tomalesbaywatershed.org . To ensure continued community involvement in the development and implementation of a Stewardship Plan for the Tomales Bay watershed, the Council reached out to the local community during February through June of 2003 to solicit feedback on the Draft Plan. During this campaign, the Council presented the Draft Plan directly to many community organizations, hosted 3 community meetings, and a meeting of agency representatives to solicit public feedback on the Plan. Many important questions and comments were raised during this public outreach campaign, which provided the Council with valuable information to be included in the Final Stewardship Plan. The Council reviewed each comment and collectively decided, through a consensus-based approach, how to incorporate these recommendations into the Final Plan. Specifically, many technical writing and editing suggestions were provided to improve the clarity. Questions and comments were submitted about specific projects and programs, as well as the future role of the Council, and some provided the Council with priority recommendations to achieve the goals of the Plan while supporting the overall mission to enhance community stewardship. In some instances, no action was taken and/or the issue has been recorded for future consideration. 1. Does Council envision taking on a regulatory, enforcement or political role? At this time, the Council believes the greatest resource protection benefit will be gained by forming collaborative partnerships with community groups and agency partners to guide specific restoration projects and enhance stewardship within the watershed as described in the Stewardship Plan. In addition, the Council is a community-based organization that does not have direct authority to implement or enforce regulations. However, many federal, state and local agency representatives with regulatory authority hold seats on the Council; therefore the Council represents an important forum for the discussion of current regulation and/or enforcement actions within the watershed. In the future, as specific activities are ongoing, the Council may determine that additional regulations and/or additional enforcement measures are necessary to enhance resource protection. At that time, the Council will work with agency partners and community residents to define the policy role the Council can take to further enhance resource protection.

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2. The Plan should include indicators so that the Plan's success in achieving its goals can be measured. A major goal contained in the Stewardship Plan is to reduce sources of water pollutants with the specific objective of removing Tomales Bay from the 303(d) list of impaired waterbodies as designated by the Regional Water Quality Control Board. The Council believes that improved water quality is the most beneficial objective to restore the integrity of diverse and sensitive habitats and populations of local and migratory wildlife, while continuing to ensure sustainable human activities in the watershed. As specific projects and programs are designed and implemented, the Council will ensure that particular criteria are developed to define project goals, measuring success either qualitatively or quantitatively. Projects will be designed to achieve the specific goals and objectives contained within the Stewardship Plan. 3. Will the Council be actively involved in carrying out projects or primarily a forum for discussion of projects? Please see the Council’s priorities for 2003-2006 in Section IV, Part B. in the Plan. The Council’s primary objectives are to create collaborative partnerships to restore the natural integrity of the watershed and to support active community stewardship. As the Council considers specific projects and programs needed to meet the goals and objectives of the Plan, the necessary community and agency partnerships and stewardship activities will be formed to implement these projects and programs. If it is determined that a partnership does not exist, or no specific community group or agency is able to lead the implementation of a specific project, or that it would not be feasible to create a partnership to implement a specific project or program, the Council will then determine its willingness to carry out that specific project or program. Currently, the Council has committed to developing a comprehensive water quality monitoring plan as it is the most appropriate forum to design such a program and to work with stakeholders in the watershed to ensure successful implementation. The Council is also working with individual organizations and agencies to facilitate effective and meaningful assessment and restoration of natural habitats such as the Lagunitas Creek Watershed Improvement Program with the RCD and other community partners. Outreach and education will continue to be an on-going function of the Council in the future. 4. What are the specific projects in the plan to reduce non-point source pollution? Action 2.0 “Support implementation of practices and projects that will reduce nonpoint sources of water pollution and enhance habitats in Tomales Bay and its watershed” of the Stewardship Plan contains many priority projects to be conducted on public and private lands to support the implementation of best management practices to reduce non-point sources of pollution. In addition, Action 4.0 “Promote and support public outreach and education about Tomales Bay and its watershed,” includes many community educational and outreach activities that will further assist in the reduction of non-point sources of pollution entering Tomales Bay and its watershed. Tomales Bay Watershed Stewardship Plan: A Framework for Action 133

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5. What do we do about effects from natural siltation? The Council understands and recognizes the natural process of siltation that occurs in tributaries and the bay, and throughout the watershed. The Stewardship Plan was developed to identify and address human activities that increase sedimentation. The Plan contains specific recommendations for activities and improved management practices designed to reduce, to the maximum extent possible, human-induced sources of sedimentation and reduced water quality that affects the natural conditions within Tomales Bay and its tributaries. 6. The Plan contains a lot of studies. How do we get to implementation of specific restoration projects quicker? The Stewardship Plan is designed as a framework to guide the development and implementation of specific projects and programs necessary to improve management practices and sustain beneficial uses within the watershed. The Council has identified both priority studies and specific projects within the four Actions contained within the Stewardship Plan. Two major studies detailed in Action 1.0 “Develop a coordinated and comprehensive water quality monitoring plan for Tomales Bay and tributary streams,” and Action 3.0 “Assess, protect and restore key habitats for species of local interest,” include the development of a water quality monitoring program and the development of a habitat and species database, respectively. After extensive community discussion, the Council determined that these studies were necessary to identify current activities taking place and future project needs in order to ensure that individual on-going projects are designed to be compatible and improve our collective understanding of issues within the watershed. In addition, many specific projects are prioritized in Action 3 to implement BMPs on public and private lands thus reducing non-point source pollution. Action 4 contains specific education and outreach projects to increase community awareness about the issues that affect Tomales Bay and its watershed, identified by the Council as essential to improve our collective understanding and support stewardship. Additionally, Appendix B: Erosion and Sedimentation in the Tomales Bay Watershed includes a preliminary list of assessment and project needs as a starting point for future planning discussions. The Council will work with watershed partners in the next 12 months to identify specific projects and leads for each project, in addition to funding needs and potential sources. 7. What is the TBWC targeted annual budget? TBWC fundraising committee is currently developing the long-term budgetary needs for the Council including a targeted annual budget. Currently, the Council has the financial support to operate at its current capacity for the next 2 years (approximately $60-70,000 per year). In the future, the Council hopes to increase its capacity to support continued improvement in watershed management in Tomales Bay.

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8. Is the TBWC working to include watershed management into the Marin County-wide plan? The Council has been working closely with Marin County staff to incorporate specific recommendations from the Stewardship plan into the County Master Watershed Plan. In addition, several Marin County representatives are Council members, thus enhancing communication and collaboration of watershed management strategies into future programs at the County level. 9. TBWC should help Marin County by updating water quality and habitats databases. The Council has identified two priority projects, Action 1.0 “Develop a coordinated and comprehensive water quality monitoring plan for Tomales Bay and tributary streams,” and Action 3.0 “Assess, protect and restore key habitats for species of local interest” in the Stewardship Plan. Specifically, Action 1.0 outlines the necessary steps to develop a comprehensive water quality monitoring program while Action 3.0 contains a high priority activity to inventory and map the distribution of key habitats and species in the watershed. The initial steps of creating such programs include the collection of pertinent data, and identification of on-going programs. To this end, start-up will integrate the latest technical documents, which will include local, state and federal monitoring and assessment information. These programs will depend on collaboration and will work to maximize efficiency and effectiveness, including compatibility issues, etc. These specific projects will significantly enhance our collective understanding of the current scientific data necessary to improve project planning to ensure successful ecological restoration of Tomales Bay at both the watershed and County level. In addition, the Council may identify future data management programs to be conducted with the County that may be necessary to increase restoration efforts in the region. 10. Are there other watershed groups that can be seen as a model for TBWC? The Council has looked at many different community groups through California as models for environmental stewardship. Because of the uniqueness of the community and natural resources of the Tomales Bay watershed a model of exact fit cannot be found. For example, the S.F. Estuary Institute, which oversees and coordinates a long-term water quality monitoring program for San Francisco Bay, or the Morro Bay and Tillamook Bay National Estuary Programs can be used as models for developing a comprehensive and coordinated water quality monitoring program for Tomales Bay. The Council will continue to work with established watershed programs such as these to incorporate specific program components that advance the Council’s mission. 11. Plan should aim to reduce conflict between community and user groups. The Council strongly agrees with this suggestion. The Council was formed to provide a forum for communication within the Tomales Bay watershed community and to develop collaborative partnerships to implement the necessary projects to restore water quality in the region. The Stewardship Plan was developed through a consensus-based process by the members of the Council, along with many active community participants. The Council believes this process helps to strengthen the goals of the Stewardship Plan by focusing on our collective goals, and through reducing conflict by increasing our understanding of the issues. Tomales Bay Watershed Stewardship Plan: A Framework for Action 135

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In addition, the Council strongly encourages continued community participation in the process to ensure that future efforts by the Council continue to diminish conflicts and enhance community stewardship. 12. The Council needs to conduct economic impact studies prior to project implementation. As the Council and its partners begin to design and implement specific projects, the public will have the opportunity to work closely with the Council to assure projects do not have inadvertent negative economic effects. In addition, any restoration project undertaken by a federal agency or under a federal grant must follow the National Environmental Policy Act (NEPA), which requires an environmental assessment of the affected region including the social and economic impacts that may occur. Also, the California Environmental Quality Act (CEQA) requires the all public agencies and projects requiring permitting and approval by any public agency to determine whether a project will have negative environmental impacts and list ways in which these negative impacts can be minimized. Both the NEPA and CEQA processes include extensive opportunities for the public to provide their input to assure that a project does not create negative socio-economic impacts in the affected region. 13. Need to better educate the public on water quality issues and include watershed education into local schools. Many recommendations were provided to the Council on education and outreach programs to better educate the community on current water quality issues such as the Pathogen TMDL (a water pollution reduction plan recently developed by the Regional Water Quality Control Board to reduce pathogen levels in Tomales Bay and tributaries in the watershed). Where appropriate the Council has included these recommendations into the prioritized activities in Action 4.0 “Promote and support public outreach and education about Tomales Bay and its watershed.” The Council will consider these as important recommendations from the community. 14. Indicator tests do not indicate source of pollutants. Current scientific research indicates that coliform is the best indicator organism of pathogens in polluted water for shellfish growing and recreational water use. Techniques for direct monitoring of pathogens in waterbodies are known but are not yet considered reliable indictors. Although the scientific community is aware of the shortcomings of fecal coliform as an indicator of pathogens, such as not indicating source, it is acknowledged at this time that it is the best indicator of pathogens in a waterbody that currently exists. 15. Recommendations were made to provide more information on regulatory framework and current activities and community groups working in the watershed. The Council has included a list of federal state, and local laws as a regulatory framework for activities in the region in Section I of the Stewardship Plan. Due to limited time and funding a more comprehensive list of regulations and governmental programs taking place in the watershed is not able to be included in the final Plan. However, an activity has been included in Action 4.0 to develop a watershed directory to provide current programs, volunteer and outreach activities, and contact information for agencies and organizations currently working Tomales Bay Watershed Stewardship Plan: A Framework for Action 136

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in the region. The Council believes this watershed directory will provide a more extensive list of regulatory authorities and of current programs necessary for better coordination of future stewardship efforts. 16. The Plan should address alternative transportation such as bicycle use to reduce runoff into the bay. The Council has not considered transportation in its planning activities to date, however the water quality associated impacts of road traffic and the Marin County Stormwater Program (MCSTOPPP) have been incorporated into Appendix A: Water Quality Status and Trends Report. Transportation and road traffic are clearly significant issues in the watershed, and the Council will consider this issue in the future and evaluate how it is currently being managed and the potential need for additional attention. 17. The Plan should contain a statement that affordable housing is aligned with the protection of the watershed. The Council has not considered affordable housing in the development of this watershed stewardship plan. The Council will consider this issue in the future and evaluate how it is currently being addressed, and the potential need for additional attention as it relates to the Council’s vision and goals for the watershed.

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