SF_Bay_NRMP_clean_20191120_0001.pdf

Natural Resource Management Plan for the San Francisco Bay National Wildlife Refuge Complex

September 2019

“The conservation landscape has changed, the playing field has changed and the stakes have changed. Human demands on the environment combined with environmental stressors are creating an urgent need for conservation choices. The scale of issues and challenges we face is unprecedented and impacts us all; no single entity has the resources necessary to address these challenges on its own. Conserving the Future acknowledges that strategic, collaborative, science-based landscape conservation—along with effective public outreach, education and environmental awareness—is the only path forward to conserve America's wildlife and wild places.”

CONSERVING THE FUTURE: WILDLIFE REFUGES AND THE NEXT GENERATION (USFWS 2011)

ON THE COVER

From left to right, top to bottom

California tiger salamander (Ambystoma californiense), USFWS Tidal marsh, Judy Irving © Pelican Media

Western snowy plover (Charadrius alexandrinus nivosus), © Aric Crabb, Bay Area News Group Farallon Islands, Brian O’Neil

Marin Islands National Wildlife Refuge, USFWS Lange’s metalmark butterfly (Apodemia mormo langei), USFWS

Children restoring native plants, Student and Teachers Restoring a Watershed, (Point Blue Conservation Science)

Marbled godwits and willets, Judy Irving © Pelican Media Vernal pool grasslands, USFWS

CITATION:

U.S. Fish and Wildlife Service. 2019. Natural Resource Management Plan for the San Francisco Bay National Wildlife Refuge Complex. National Wildlife Refuge System, Pacific Southwest Region, Sacramento, CA.

Natural Resource Management Plan San Francisco Bay National Wildlife Refuge Complex i

Contents

San Francisco Bay National Wildlife Refuge Complex Natural Resource

Management Plan

Signatures i

Abbreviations ......................................................................................................................................................... vii

Abstract .................................................................................................................................................................... ix

Chapter 1—Introduction

1.1 The San Francisco Bay National Wildlife Refuge Complex

1.2 Refuge Conservation Planning: Past and Present

1.3 Plan Purpose, Need, and Objectives

1.4 Physiographic and Ecological Summary of the Region

1.4.1 San Francisco Bay Region

1.4.2 Monterey Bay Region

1.4.3 Farallon Islands

Chapter 2—Methods

2.1 Project Team

2.2 Planning Approach

2.2.1 Identifying Priority Natural Resources of Concern

2.2.2 Planning Process and Timeline

2.2.3 Terminology

Chapter 3—Summary of Results

3.1 Conservation Scope

3.2 Conservation Targets

3.4 Target Viability and Goals

3.5 Critical Threats

3.5.1 Climate Change

3.5.2 Conceptual Models

3.6 Management Strategies

3.6.1 Refuge Complex Strategy: Invasive Plant Management

3.6.2 Refuge Complex Strategy: Data Management

3.7 Inventory, Monitoring, and Research

3.8 Work Plan

Chapter 4—Conservation Target Summaries

4.1 Coastal Sand Dune Ecosystem

4.1.1 Overview

4.1.2 Ecology

4.1.3 Target Status, Trends, and Goals

4.1.4 Critical Threats

4.1.5 Conservation Strategies and Objectives

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4.1.6 Natural Resource Surveys

4.2 Estuarine Island Ecosystem

4.2.1 Overview

4.2.2 Ecology

4.2.3 Target Status, Trends, and Goals

4.2.4 Critical Threats

4.2.5 Conservation Strategies

4.2.6 Natural Resource Surveys

4.3 Marine Island Ecosystem

4.3.1 Overview

4.3.2 Ecology

4.3.3 Target Status, Trends, and Goals

4.3.4 Critical Threats

4.3.5 Conservation Strategies

4.3.6 Natural Resource Surveys

4.4 Pajaro Valley Watershed

4.4.1 Overview

4.4.2 Ecology

4.4.3 Target Status, Trends, and Goals

4.4.4 Critical Threats

4.4.5 Conservation Strategies

4.4.6 Natural Resource Surveys

4.5 Riverine Sand Dune Ecosystem

4.5.1 Overview

4.5.2 Ecology

4.5.3 Target Status, Trends, and Goals

4.5.4 Critical Threats

4.5.5 Conservation Strategies

4.5.6 Natural Resource Surveys

4.6 Tidal Marsh Ecosystem

4.6.1 Overview

4.6.2 Ecology

4.6.3 Target Status, Trends, and Goals

4.6.4 Critical Threats

4.6.5 Conservation Strategies

4.6.6 Natural Resource Surveys

4.7 Vernal Pool Grassland Ecosystem

4.7.1 Overview

4.7.2 Ecology

4.7.3 Target Status, Trends, and Goals

4.7.4 Critical Threats

4.7.5 Conservation Strategies

4.7.6 Natural Resource Surveys

4.8 Waterbirds

4.8.1 Overview

4.8.2 Ecology

4.8.3 Target Status, Trends, and Goals

4.8.4 Critical Threats

4.8.5 Conservation Strategies

4.8.6 Natural Resource Surveys

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Chapter 5—Human Well-Being Target Summaries

5.1 Overview

5.2 Human Well-Being Targets

5.2.1 Wildlife-Dependent Recreation

5.2.2 Culture, Community, and Heritage

5.2.3 Mental and Physical Well-Being

5.2.4 Increased Knowledge and Awareness

5.3 Viability of the Human Well-Being Targets

5.3.1 Wildlife-Dependent Recreation

5.3.2 Culture, Community, and Heritage

5.3.3 Mental and Physical Well-Being

5.3.4 Increased Knowledge and Awareness

5.4 Threats to the Human Well-Being Targets

5.4.1 Insufficient Amenities

5.4.2 Lack of Interest

5.4.3 Lack of Knowledge and Awareness

5.4.4 Language Barrier

5.4.5 Trash and Vandalism

5.4.6 Lack of ADA/ABA Accessible Infrastructure

5.4.7 Lack of Staff Knowledge

5.4.8 Competition

5.4.9 Personal Income

5.4.10 Wayfinding Challenges

5.4.11 Staff Perception

5.4.12 Fear of Nature

5.5 Strategies to Support Human Well-Being

5.5.1 Conduct Environmental Education in Schools

5.5.2 Conduct Environmental Education and Interpretation with Community Groups

5.5.3 Conduct Habitat Restoration-Learning Programs

5.5.4 Enhance and Manage a Volunteer Program

5.5.5 Conduct Strategic Communications to Affect Behavior Change

5.5.6 Conduct Community Outreach Offsite with (New) Target Audiences

5.5.7 Conduct Patrols and Increase Staff or Volunteer Presence in Public Areas

5.5.8 Improve Communication on How to Get around the Refuge (once here)

5.5.9 Improve and Maintain Visitor Amenities

5.6 Urban Wildlife Conservation Program—Standards of Excellence

5.7 Priority Surveys for the Human Well-Being Targets

Chapter 6—Plan Implementation and Evaluation

6.1 Annual Evaluation and Work Planning

6.2 Balancing Commitments

6.2.1 Central Coast Common Murre Restoration Project

6.2.2 Alameda Point California Least Tern Colony Management

6.2.3 Haying/Grazing Program

6.2.4 Permit Monitoring Requirements

6.2.5 Landscape Conservation

6.3 Management Changes and Consequences

6.3.1 Farallon Islands National Wildlife Refuge

6.3.2 Don Edwards San Francisco Bay National Wildlife Refuge

6.3.3 Salinas River National Wildlife Refuge

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6.3.4 San Pablo Bay National Wildlife Refuge

6.3.5 Ellicott Slough National Wildlife Refuge

6.3.7 Marin Islands National Wildlife Refuge

6.3.6 Antioch Dunes National Wildlife Refuge

Literature Cited Chapter 1—Introduction Chapter 2—Methods Chapter 3—Summary of Results Chapter 4—Conservation Target Summaries Chapter 5—Human Well Being Target Summaries Chapter 6—Plan Implementation and Evaluation

Appendix A

Appendix B

FIGURES

Figure 1. Conservation Measures Partnership’s Open Standards process. Source: Open Standards for the Practice of Conservation (Conservation Measures Partnership 2013) Figure 2. Geographic setting of the seven refuges of the San Francisco Bay National Wildlife Refuge Complex Figure 3. Salinas River National Wildlife Refuge and surrounding protected lands in Monterey Bay, California Figure 4. Landcover types and adjacent lands of Salinas River National Wildlife Refuge Figure 5. Conceptual model of the coastal sand dune ecosystem at Salinas River National Wildlife Refuge Figure 6. Geographic setting of Marin Islands National Wildlife Refuge and State Ecological Reserve Figure 7. Conceptual model of the estuarine island ecosystem at Marin Islands National Wildlife Refuge Figure 8. Geographic setting of Farallon Islands National Wildlife Refuge Figure 9. Change in estimated population size index of ashy storm-petrels over time at Farallon Islands National

Wildlife Refuge, based on captures of individually-banded ashy storm-petrels, 1999–2016 Figure 10. The maximum total count of northern fur seals (NFS), harbor seals (HS), California sea lions (CSL), and stellar sea lions (SSL), 1970–2015 Figure 11. Conceptual model of the marine island ecosystem at Farallon Islands National Wildlife Refuge Figure 12. Conceptual model of the marine island ecosystem at Farallon Islands National Wildlife Refuge depicting the most critical threats and strategies aimed at addressing them Figure 13. Map depicting location and hydrological features of the Pajaro Valley watershed and Ellicott Slough

National Wildlife Refuge Figure 14. Geographic setting of Ellicott Slough National Wildlife Refuge and associated management units, Santa Cruz County, California Figure 15. Conceptual model of the Pajaro Valley watershed Figure 16. Geographic setting of Antioch Dunes National Wildlife Refuge, Contra Costa County, California Figure 17. Timeline of events and trends in peak Lange’s metalmark butterfly counts and fire at Antioch Dunes

National Wildlife Refuge, 1982–2015 Figure 18. Acres burned by fire (red line) and LMB peak counts (orange bars) over time in the Sardis and Stamm

Units Figure 19. Conceptual model of the riverine dune ecosystem at Antioch Dunes National Wildlife Refuge Figure 20. Geographic setting of Don Edwards San Francisco Bay National Wildlife Refuge Figure 21. Geographic setting of San Pablo Bay National Wildlife Refuge v

Figure 22. Conceptual model of the tidal marsh ecosystem at Don Edwards San Francisco Bay and San Pablo Bay National Wildlife Refuges

Figure 23. Vernal pools monitored for hydroperiod, California tiger salamander (CTS) and vernal pool tadpole shrimp (VPTS) in the Warm Springs Subunit (Mowry Unit) at Don Edwards San Francisco Bay National Wildlife Refuge

Figure 24. Conceptual model of the vernal pool grassland ecosystem at Don Edwards San Francisco Bay National Wildlife Refuge depicting natural resource threats and strategies aimed at addressing the most critical threats (ranked High or Very High)

Figure 25. Conceptual model of waterbirds for Don Edwards San Francisco Bay (SFB), San Pablo Bay (SNP), and Marin Islands (MRI) National Wildlife Refuges depicting natural resource threats and strategies aimed at addressing the most critical threats (ranked High or Very High). The letters in the upper left portion of threats (pink boxes) represent the summary threat ranking across the seven refuges of the San Francisco National Wildlife Refuge Complex (L=low, M=moderate, H=high, VH=very high)

Figure 26. Conceptual model of human well-being benefits connected to conservation targets of the San Francisco Bay National Wildlife Refuge Complex

Figure 27. Conceptual model of the four human well-being targets across the San Francisco Bay National Wildlife Refuge Complex depicting the most critical threats and strategies aimed at addressing them

TABLES

Table 1. Project team for the San Francisco Bay National Wildlife Refuge Complex Natural Resource

Management Plan Table 2. Schedule of workshops used to inform the San Francisco Bay National Wildlife Refuge Complex Natural

Resource Management Plan Table 4. Priority conservation targets and nested targets of the San Francisco Bay National Wildlife Refuge

Complex (listed in alphabetical order) Table 5. Status of conservation targets (N=8) across the seven refuges of the San Francisco Bay National

Wildlife Refuge Complex Table 6. Biological conservation targets and priority strategies employed to conserve them within the San

Francisco Bay National Wildlife Refuge Complex: FY2018–2022 Table 7. Human-induced threats to priority conservation targets (N=8) of the San Francisco Bay National Wildlife

Refuge Complex Table 8. Current status and desired future state (goals) of the coastal sand dune ecosystem at Salinas River

National Wildlife Refuge in terms of key ecological attributes and indicators Table 9. Salinas River National Wildlife Refuge strategies and associated objectives, in order of priority to implement over the next 5 years (2018–2022) to conserve the coastal dune ecosystem Table 10. Natural resource surveys that will inform progress in achieving coastal dune ecosystem goals and objectives (Salinas River National Wildlife Refuge) Table 11. Current status and desired future state (goals) of the estuarine island ecosystem at Marin Islands

National Wildlife Refuge in terms of key ecological attributes and indicators Table 12. Native orchid species of Marin Islands National Wildlife Refuge: taxonomy, range, special status designations, and habitat Table 13. Marin Islands National Wildlife refuge management strategies and associated objectives, in order of priority to implement over the next 5 years to conserve the estuarine island ecosystem Table 14. Natural resource surveys to inform progress in achieving estuarine island ecosystem goals and objectives (Marin Islands National Wildlife Refuge) Table 15. Population trend (2012–2016) of five breeding seabird species at Southeast Farallon Island and West

End Island, Farallon Islands National Wildlife Refuge (2012–2016) Table 16. Current status and desired future state (goals) of the marine island ecosystem at Farallon Islands

National Wildlife Refuge in terms of key ecological attributes and indicators Table 17. Farallon Islands National Wildlife Refuge management strategies and associated objectives, in order of priority to implement over the next 5 years to conserve the marine island ecosystem

Table 18. Natural resource surveys to inform progress in achieving marine island ecosystem goals and objectives (Farallon Islands National Wildlife Refuge)

Table 19. Current status and desired future state (goals) of the Pajaro Valley watershed at Ellicott Slough National Wildlife Refuge in terms of key ecological attributes and indicators

Table 20. Ellicott Slough National Wildlife Refuge management strategies and associated objectives, in order of priority to implement over the next 5 years (2018–2022) to help conserve the Pajaro Valley watershed

Table 21. Natural resource surveys to inform progress in achieving Pajaro Valley watershed goals and objectives (Ellicott Slough National Wildlife Refuge)

Table 22. Current status and desired future state (goals) of the riverine dune ecosystem at Antioch Dunes National Wildlife Refuge in terms of key ecological attributes and indicators

Table 23. Antioch Dunes National Wildlife Refuge management strategies and associated objectives, in order of priority to implement over the next 5 years (2018–2022) to help conserve the riverine dune ecosystem

Table 24. Natural resource surveys to inform progress in achieving riverine dune ecosystem goals and objectives (Antioch Dunes National Wildlife Refuge)

Table 25. Current status and desired future state (goals) of the tidal marsh ecosystem at Don Edwards San Francisco Bay and San Pablo Bay National Wildlife Refuges in terms of key ecological attributes and indicators

Table 26. Tidal marsh ecosystem management strategies and associated objectives, in order of priority to implement over the next 5 years

Table 27. Natural resource surveys to inform progress in achieving tidal marsh ecosystem goals and objectives at Don Edwards San Francisco Bay and San Pablo Bay National Wildlife Refuges

Table 28. Number of pools containing California tiger salamander and vernal pool tadpole shrimp in relation to vernal pool hydroperiod (pool inundation) at the Warm Springs Subunit of Don Edwards San Francisco Bay National Wildlife Refuge, 2012–2015

Table 29. Current status and desired future state (goals) of the vernal pool grassland ecosystem at Don Edwards San Francisco Bay National Wildlife Refuge in terms of select indicators

Table 30. Vernal pool grassland ecosystem conservation strategies and associated objectives Table 31. Vernal pool grassland ecosystem natural resource surveys to inform management effectiveness and progress on goals and objectives Table 32. Current status and desired future state (goals) of waterbirds at Don Edwards San Francisco Bay

National Wildlife Refuge, Marin Islands National Wildlife Refuge, and San Pablo Bay National Wildlife Refuge in terms of select indicators

Table 33. Threats to nested waterbird targets at San Pablo Bay NWR, Don Edwards San Francisco Bay NWR, and Marin Islands NWR

Table 33. Waterbird management strategies and associated objectives, in order of priority to implement over the next 5 years

Table 34. Estuarine island ecosystem natural resource surveys to inform management effectiveness and progress on goals and objectives

Table 35. Ecosystem services provided by conservation targets Table 36. Current status and desired future state (goals) of the human well-being targets for the San Francisco

Bay National Wildlife Refuge Complex in terms of select indicators Table 37. Selected threats per human well-being target Table 38. Threats addressed by each strategy and expected outcomes (objectives) Table 39. Human well-being strategies and contributions to Standards of Excellence Table 40. Surveys linked to human well-being goals and objectives in the San Francisco Bay National Wildlife

Refuge Complex 5-year work plan Table 41. Landscape conservation partnerships of the San Francisco Bay National Wildlife Refuge Complex vii

Abbreviations

Abbreviations

ADEP Antioch Dunes evening primrose BCDC San Francisco Bay Conservation and Development Commission BRRIT Bay Restoration Regulatory Integration Team

CCP comprehensive conservation plan CCW Contra Costa wallflower

CDFW California Department of Fish and Wildlife CLMA cooperative land management agreement CNPS California Native Plant Society

CTS California tiger salamander Estuary San Francisco Estuary

HSU Humboldt State University IMP inventory and monitoring plan ISP San Francisco Estuary Invasive Spartina Project

KEA key ecological attribute or key engagment attribute LMB Lange’s metalmark butterfly

MHHW mean higher high water MHW mean high water

NEPA National Environmental Policy Act NRMP natural resource management plan NWR national wildlife refuge

OSPR California Department of Fish and Wildlife’s Office of Spill Prevention and Response refuge national wildlife refuge Refuge Complex San Francisco Bay National Wildlife Refuge Complex

Refuge System National Wildlife Refuge System RIRA Ridgway’s rail ROC resource of concern SBB Smith’s blue butterfly

SCEP Sonoma Creek Marsh Enhancement Project SCLTS Santa Cruz long-toed salamander

SEFI Southeast Farallon Island, Farallon Islands National Wildlife Refuge Service U.S. Fish and Wildlife Service SFBBO San Francisco Bay Bird Observatory

SFI South Farallon Islands , Farallon Islands National Wildlife Refuge SMHM salt marsh harvest mouse SNPL western snowy plover USDA U.S. Department of Agriculture

USFWS U.S. Fish and Wildlife Service VPTS vernal pool tadpole shrimp ix

Executive Summary

Abstract

Over the past 2 decades, the U.S. Fish and Wildlife Service (Service) developed a comprehensive conservation plan (CCP) for each of the seven refuges in the San Francisco Bay National Wildlife Refuge Complex (Refuge Complex): Antioch Dunes, Don Edwards San Francisco Bay, Ellicott Slough, Farallon Islands, Marin Islands, Salinas River, and San Pablo Bay. The CCPs describe desired future conditions at each refuge and provide long-range guidance and management direction to achieve refuge purposes, help fulfill the National Wildlife Refuge System mission, and maintain or restore the ecological integrity of the refuge. Several factors have affected our ability to achieve all conservation goals and objectives laid out in CCPs, however. These factors include significant declines in federal funding and staffing levels over the past several years (at least since fiscal year 2010), a changing landscape in the context of human demands on the environment, and environmental stressors such as invasive species and climate change. Subsequently, as we persist to “do more with less” in ways that are “how we’ve always done it,” we face uncertainties due to increasing workloads and a lack of clear priorities. To address these challenges and promote a more adaptive, evidence-based approach to conservation within the Refuge Complex, the Service is taking a new approach, specifically in how we make decisions and deploy limited resources optimally to help us achieve our conservation mission. This approach involves 1) identification of natural resource conservation priorities (also known as priority resources of conservation concern or conservation targets), 2) refinement of conservation goals and objectives so that it’s crystal clear what conservation success looks like, 3) identification of the highest priority management strategies— most likely to lead to achieving stated goals and objectives, 4) identification of the highest priority surveys needed to evaluate progress in achieving goals and objectives, and 5) instituting a regular practice of evaluation, learning, and adaptation through annual work planning and evaluation. The methods and results of this new conservation approach are presented in this Natural Resource management Plan (NRMP), a companion inventory and monitoring plan (IMP), and a 5-year work plan. The NRMP also describes how human well-being will benefit from natural resource conservation in the Refuge Complex and lays out specific strategies to build public support and stewardship for natural resource conservation and advance the Service’s mission to connect people with nature. The IMP provides details about surveys needed to evaluate conservation progress, and the 5-year work plan provides operational details needed for implementation and evaluation.

Together, the NRMP, IMP, and 5-year work plan provide a foundation for focusing limited resources where they are most needed, help institute a more evidence-based approach to conservation, promote more realistic staff workloads, and ultimately increase our likelihood of conservation success in a rapidly changing world.

Chapter 1—Introduction

1.1 The San Francisco Bay National Wildlife Refuge Complex

The National Wildlife Refuge System (Refuge System) was established in 1903 with the designation of the first bird reserve by President Theodore Roosevelt at Pelican Island, Florida. The mission of the Refuge System was reaffirmed in the National Wildlife Refuge System Improvement Act of 1997 “to administer a national network of lands and waters for the conservation, management and, where appropriate, restoration of the fish, wildlife and plant resources and their habitats within the United States for the benefit of present and future generations of Americans.” As of September 30, 2018, the Refuge System constitutes the world’s largest conservation area network, comprising 562 national wildlife refuges and 38 wetland management districts totaling over 150 million acres. The Refuge System is administered by the U.S. Fish and Wildlife Service (Service), a bureau of the U.S.

Department of the Interior.

The San Francisco Bay National Wildlife Refuge Complex (Refuge Complex) consists of seven national wildlife refuges (NWRs) (listed in order of establishment): Farallon Islands NWR (1909), Don Edwards San Francisco Bay NWR (1972), Salinas River NWR (1973), San Pablo Bay NWR (1974), Ellicott Slough NWR (1975), Antioch Dunes NWR (1980), and Marin Islands NWR (1992).

Due to the refuges’ geographic proximity and common challenges, the Service organized these refuges as a Refuge Complex for administrative purposes.

These refuges were established in response to declining wildlife populations from commercial harvesting that began in the late 19th century and rapid habitat loss from human development that ramped up in the mid-20th century. Now these refuges protect a variety of wetland and associated upland habitats that support nesting, foraging, wintering, and resting points for millions of migratory birds along the Pacific Flyway. The refuges also provide vital habitat for several species of birds, mammals, insects, amphibians, and plants that are federally listed or state-listed as threatened or endangered, as well as other species of concern. Unlike most other NWRs, which are predominantly in rural or remote locations, these seven refuges share the challenge of pursuing wildlife conservation objectives in the midst of highly urbanized areas. Today, the San Francisco– Monterey Bay area is home to nearly 9 million people across 11 counties and more than 100 incorporated cities spread over some 10,000 square miles, including the major metropolitan areas of San Francisco, Oakland, and San Jose.

1.2 Refuge Conservation Planning: Past and Present

The Service completed comprehensive conservation plans (CCPs) for each of the seven refuges in the Refuge Complex to guide management over a 15-year period, pursuant to the 1997 Improvement Act.1 Each CCP describes the refuge history and ecology of its natural resources and lays out the desired future conditions and long-range guidance to accomplish the purposes for which each refuge was established. The comprehensive conservation planning process helps the Service achieve the refuge purposes and the Refuge System mission by identifying goals, objectives, and strategies to implement at each refuge, including proposed staffing and funding levels necessary to fulfill the goals. The CCPs and accompanying environmental assessments address Service legal mandates, 1 The CCPs can be accessed at https://ecos.fws.gov/ServCat/Search/Advanced/17.

https://ecos.fws.gov/ServCat/Search/Advanced/17 policies, goals, and National Environmental Policy Act (NEPA) compliance. The Service acknowledges that the strategies identified in CCPs may exceed current budget allocations and do not guarantee a commitment of resources.

We (Refuge Complex staff) have been implementing various strategies consistent with the goals and objectives originally identified for each refuge; however, several factors have affected our ability to fully focus on the most effective strategies and assess outcomes. These factors include significant declines in federal funding and staffing levels over the past several years (at least since fiscal year 2010), a changing landscape in the context of human demands on the environment, and environmental stressors such as invasive species and climate change. Subsequently, as we persist to “do more with less” in ways that are “how we’ve always done it,” we face uncertainties due to increasing workloads and lack of clear priorities. We must reflect on the work we have done and consider new approaches in how we make decisions and deploy limited resources optimally to refocus on the most important strategies and natural resource surveys with greatest likelihood of helping us achieve our conservation mission.

1.3 Plan Purpose, Need, and Objectives

Inspired by the Service’s 21st century strategic vision for the Refuge System, Conserving the Future:

Wildlife Refuges and the Next Generation (USFWS 2011), we approached our refocusing task by considering the unique ecosystems represented by individual refuges within the broader landscape conservation context of the San Francisco–Monterey Bay Area. Using the Open Standards for the Practice of Conservation (Open Standards; Conservation Measures Partnership 2013) as a structured priority-setting process, we developed a natural resource management plan (NRMP) and its companion inventory and monitoring plan (IMP). A step-down management plan from the CCP, this NRMP serves as the refuge’s habitat management plan, pursuant to Service policy (620 FW 1).

While CCPs identify overarching refuge management goals, objectives, and strategies for a particular refuge, habitat management plans “step down” the direction provided in a CCP to provide refuge managers with more specific guidance and prescriptions for the implementation of management strategies on refuge lands. The NRMP identifies priority resources of concern in the Refuge Complex (hereafter referred to as conservation targets), and associated priority strategies to conserve them given limited resources. We recognize that the health of the conservation targets provides various ecosystem services that benefit humans; accordingly, a unique aspect of this NRMP is its inclusion of human well-being targets that directly link to conservation targets. For example, wetlands provide regulating services such as pollutant filtration and flood protection. Ecosystems also provide cultural services, non-material benefits that people derive through recreation, aesthetic or spiritual enrichment, and education. By assessing a range of human well-being targets, we identified several strategies for public engagement that will be essential for addressing many threats to our conservation targets. Conservation targets are detailed in chapter 4. Priority human well-being targets are detailed in chapter 5.

One of the most important elements of the NRMP is the provision of specific, measurable, results-oriented, and time-bound goals and objectives. These goals and objectives are critical for evaluating conservation progress, learning, and adaptation. Many of these goals and objectives require surveys to assess progress in achieving goals and objectives. The companion IMP provides more detail about these surveys; it also shows the links between scientific information and management needs as well as information gaps.

On-the-ground implementation of the NRMP and IMP is guided by a 5-year work plan. The work plan lays out specific activities related to management strategies and surveys, who is responsible for carrying them out, and when they will be carried out. Together, the NRMP, IMP, and associated 5-year work plan will promote a more adaptive and evidenced-based approach to conservation in the Refuge Complex.

The desired outcomes that guided the work planning effort for the NRMP and IMP are listed in the following.

A multi-year work plan is developed for the San Francisco Bay National Wildlife Refuge Complex that— optimally allocates staffing and funding to help meet priority refuge purposes focuses on strategies and actions with the greatest conservation benefit provides a level of consistency across the refuges for developing survey protocols and integrating data for a broader perspective across the landscape links individual performance and accomplishments (roles, responsibilities, daily tasks) to priority conservation targets creates a framework for balancing workload on priority actions with building capacity to take on new opportunities and emerging issues, while also being able to justify saying “no” to non-priority projects provides a platform for annual work planning, budgeting, and performance assessment integrates all programs—biology, visitor services, maintenance, law enforcement, administration—to enhance coordination across the Refuge Complex to reach shared goals.

Refuge Complex staff and key partners have a collective understanding about the priority conservation and human well-being targets, threats/challenges, and management strategies across the Refuge Complex, and they accordingly support the processes and decisions about how to allocate limited staffing and funding resources.

Refuge Complex staff can articulate how our work aligns with the Service’s regional and national priorities, as well as within the larger landscape goals for the San Francisco– Monterey Bay Area so that we can better leverage partnership and funding opportunities.

1.4 Physiographic and Ecological Summary of the Region

California is the most biodiverse state in the United States and one of the most biodiverse regions in the world outside of the tropics (Mooney and Zavaleta 2016). California’s high level of endemism and species richness is due to its Mediterranean climate and diversity of landscapes from offshore islands, coastal lowlands, large estuaries and alluvial valleys, forested mountain ranges, and desert (Griffith et al. 2016). While more than 30% of California’s species are threatened with extinction, only a remarkable <0.3% of its native species have been driven to global extinction, perhaps in large part due to the extensive network of protected areas that cover 46% of the state’s land area (Mooney and Zavaleta 2016). It is within this context that the refuges in the San Francisco–Monterey Bay Area contribute substantially to protecting and restoring some of California’s iconic habitats and associated flora and fauna.

California encompasses 13 Level III Ecoregions, a spatial framework that recognizes areas of general similarity in ecosystems and in the type, quality, and quantity of environmental characteristics including geology, physiography, vegetation, climate, soils, land use, wildlife, and hydrology (Griffith et al. 2016). Six of the refuges in the Refuge Complex fall within the Central California Foothills and Coastal Mountains Level III Ecoregion and encompass representative samples of several habitat types found in this ecoregion, including tidal wetlands, grasslands, oak woodlands, and dunes. The seventh refuge, Farallon Islands NWR, is a group of small granitic islands located 26 miles offshore in the Pacific Ocean and falls within the Coast Range Level III Ecoregion. The following information summarizes the general ecological setting within which our refuges are situated. Chapter 4 provides more specific descriptions of the physiographic and ecological setting for each specific conservation target. Further details about the natural resources in each of the seven refuges, including historical context and lists of plant and animal species known to occur on the refuges, can be found in the refuge’s CCP.

1.4.1 San Francisco Bay Region

San Francisco Bay is the largest estuary on the west coast of the United States and one of the most important staging and wintering areas for migratory waterfowl in the Pacific Flyway. It has been designated a Western Hemisphere Shorebird Reserve Network site of hemispheric importance. Up to 1 million shorebirds can be counted foraging on the Bay’s extensive mudflats at the peak of spring migration. San Francisco Bay is also the winter home for more than 50% of the diving ducks in the Pacific Flyway, including one of the largest wintering populations of canvasbacks in North America.

The San Francisco Estuary (Estuary) contains the largest expanses of tidal marshes in California. The early 19th century tidal marsh, before substantial human impact, is estimated to have been approximately 190,000 acres (Goals Project 1999). Major alteration of the Estuary tidal marshes occurred during and after the California Gold Rush. The principal causes of tidal marsh loss were diking for agricultural uses in the North Bay and solar salt production in the South Bay. Large patches of marsh in the North Bay were diked off starting in the mid-1800s to support haying, grain production, and livestock grazing. The solar salt industry began building managed salt ponds in the mid-1850s and rapidly expanded in the 1920s–30s, eventually converting more 27,000 acres of former tidal marsh. In addition, roughly 50,000 acres of tidal marsh were filled to allow urban development, including expansion of airports, shipping ports, industry, commercial and suburban residential development, and landfills.

Today, only about 40,000 acres of tidal marsh remain, much of which occurs along the bayside fringes of levees and along the large tidal channels or mudflats. Formerly diked baylands in the North Bay are being restored back to tidal marsh, including several projects on the San Pablo Bay NWR. Managed salt ponds are still a prominent feature in the San Francisco Bay, particularly in the South Bay. The South Bay Salt Pond Restoration Project, the largest wetland restoration project on the west coast of the United States, has a goal of restoring up to 9,600 acres of former salt ponds back to tidal marsh, along with maintaining habitat (via managed ponds) for shorebirds and waterfowl, on the Don Edwards San Francisco Bay NWR. The Estuary is also home to several endemic species found nowhere else, including the Ridgway’s rail (Rallus obsoletus obsoletus;

formerly California clapper rail) (RIRA) and salt marsh harvest mouse (Reithrodontomys raviventris) (SMHM).

An important ecotone habitat between salt marshes and adjacent uplands was extensive lowland alkaline grassland with complexes of vernal pools, vernal swales, and marshes that support salt-tolerant plants. The vernal pool grasslands in the Warm Springs Subunit of the Don Edwards San Francisco Bay NWR are the only surviving representatives of this former ecotone in the Bay Area.

Another rare habitat feature within San Francisco Bay are the rocky islands, including the Marin Islands NWR. West Marin Island is home to one of the largest heron (Ardea alba, A. Herodias, Nycticorax nycticorax) and egret (Egretta thula) breeding colonies in northern California. There are no available historic data on the specific natural conditions of the Marin Islands, but they were thought to primarily consist of coast live oak woodlands, coastal sage scrub, and coastal grasslands (Baye 2005). The islands have been isolated from the mainland for approximately 3,000 years;

therefore, the remnant native flora on the Marin Islands represents a limited sample of flora once commonly found along northeastern San Francisco Bay.

Lange’s metalmark butterfly (Apodemia mormo langei) (LMB) exists entirely on the Antioch Dunes NWR, small isolated remnant sand dunes that once formed more extensively along the Sacramento–San Joaquin River but were reduced in extent and quality as a result of industrial activities such as sand mining.

1.4.2 Monterey Bay Region

The Monterey Bay region supports a broad range of habitat types including coastal dunes, wetlands, coastal chaparral, grasslands, and redwood forests. The region is a biological transition zone from southern to northern California and supports a high level of biological diversity, including many threatened and endangered species. The local climate is modified greatly by marine influence owing to its proximity to the Pacific Ocean.

Historical accounts from the mid-1800s describe the main watersheds as supporting shallow lakes, sloughs, marsh vegetation, and willow thickets, including a large wetland complex that included the lower Salinas River, Elkhorn Slough, and Pajaro River. Beginning in the 1870s, major landscape changes occurred from drainage operations and reclamation efforts that converted native habitats to agricultural production. By the 1950s, more than 90% of the region’s original wetlands had been converted to agricultural production and residential developments. Ellicott Slough NWR is located within the Pajaro Valley watershed and includes isolated ephemeral ponds that form in the hilly wooded terrain and which are heavily dependent on rainfall captured within the watershed.

Lands that now make up the Salinas River NWR were spared from conversion because of their close proximity to the ocean, susceptibility to flooding, and former military ownership. The coastal sand dunes on the Salinas River NWR represent the northern tip of a dune system that extends more than 12 miles along the Monterey Bay shoreline. The Salinas River NWR is now one of only a few places in the area where a significant expanse of wetland and riparian habitat remains.

1.4.3 Farallon Islands

Located about 26 miles offshore, the Farallon Islands’ size, topographic complexity, geologic history of isolation, and distance from other islands and the mainland have led to high endemism in flora and fauna (Mooney and Zavaleta 2016). Because of their isolation, island plant communities tend to have fewer total plant species than the mainland and are often dominated by local endemics that evolved in these unique island environments. These islands support the largest seabird breeding colony outside of Alaska as well as significant proportions of five species of pinnipeds: northern fur seal (Callorhinus ursinus), Steller sea lion, California sea lion (Zalophus californianus), harbor seal (Phoca vitulina), and northern elephant seal (Mirounga angustirostris).

The islands sit perched on the edge of the continental shelf within the California Current System, one of the most productive ecosystems in the ocean. Biodiversity of the islands is driven in large part by seasonal coastal upwelling that transports nutrients into the uppermost water depths and fuels phytoplankton blooms. These blooms support a diverse food web from zooplankton and forage fish to top predators such as seabirds, pinnipeds, and whales. Together with the waters surrounding the islands, the Farallon Islands are a critically important biodiversity hot spot protected as part of the Greater Farallones National Marine Sanctuary and included within the Golden Gate Biosphere reserve designated by the UNESCO Man and the Biosphere Programme.

Chapter 2—Methods

2.1 Project Team

This NRMP was developed by staff from the Refuge Complex and the Pacific Southwest Region Inventory and Monitoring Program (hereafter referred to collectively as the project team; table 1).

The project team consulted many other individuals, both within and outside the USFWS, to inform this NRMP and subsequent IMP. Organizations providing significant topical expertise or assistance with developing portions of this NRMP included the following.

California Landscape Conservation Cooperative Foundations of Success San Francisco Bay Wildlife Society

Table 1. Project team for the San Francisco Bay National Wildlife Refuge Complex Natural Resource Management Plan.

Name Position Primary Role in Project Erin Aceituno* GIS Specialist, Region 8 Inventory and

Monitoring Program Data support—GIS, maps

Joy Albertson Supervisory Wildlife Biologist Core planning team Melisa Amato Wildlife Refuge Specialist, San Pablo Bay NWR Human well-being team Cindy Ballard Administrative Officer Administrative team Chris Barr Deputy Refuge Complex Manager Core planning team Giselle Block* Inventory and Monitoring Specialist, Region 8 Inventory and Monitoring Program Core planning team

Don Brubaker Manager, San Pablo Bay, Antioch Dunes, and Marin Islands NWRs

Tidal marsh ecosystem, riverine dune ecosystem, estuarine island ecosystem teams

Chris Caris Wildlife Biologist Coastal dune ecosystem and Pajaro Valley watershed teams

Winnie Chan Natural Resource Planner Core planning team Ennis Chauhan Pathways Intern Human well-being team Colter Cook Education Specialist, San Francisco Bay

Wildlife Society Human well-being team

Doug Cordell Public Affairs Officer Human well-being team Rachel Esralew* Hydrologist, Region 8 Inventory and Monitoring

Program Data support: hydrology, climate change

Susan Euing Wildlife Biologist, Antioch Dunes NWR and Alameda Point

Riverine dune and waterbird ecosystem teams

Juan Flores Maintenance Worker Infrastructure maintenance team Tia Glagolev Environmental Education Specialist Human well-being team Jim Griffin Maintenance Worker Infrastructure maintenance team

Name Position Primary Role in Project Aidona Kakouros Refuge Complex Botanist Vernal pool grassland and estuarine island ecosystem teams Kaylene Keller* GIS and Data Manager and Ecologist, Region 8

Inventory and Monitoring Program Data support—resources of concern, legacy data collection

Diane Kodama Refuge Manager, Salinas River and Ellicott Slough NWRs

Coastal dune ecosystem and Pajaro Valley watershed teams

Ivette Loredo Wildlife Refuge Specialist, Don Edwards San Francisco Bay NWR

Tidal marsh ecosystem and vernal pool grassland ecosystem teams

Meg Marriott Wildlife Biologist, San Pablo Bay and Marin Islands NWR

Tidal marsh ecosystem, estuarine island ecosystem, and waterbird teams

Gerry McChesney Refuge Manager, Farallon Islands NWR Marine island ecosystem team Carmen Minch Outdoor Recreation Planner Human well-being team Genie Moore Environmental Education Specialist Human well-being team Anne Morkill Refuge Complex Manager Core planning team Paul Mueller Volunteer Coordinator Human well-being team Jesse Navarro Federal Wildlife Officer Law enforcement team Allyssa Overbay* Biological Science Technician, Region 8

Inventory and Monitoring Program Editor

Glendale Phan Federal Wildlife Officer Law enforcement team Hope Presley Interpretive Specialist, San Francisco Bay

Wildlife Society Human well-being team

Calvin Sahara Maintenance Worker Infrastructure maintenance team Jonathan Shore Wildlife Refuge Specialist, Farallon Islands NWR Marine island ecosystem team Micheal Springman Maintenance Team Leader Infrastructure maintenance team

Cheryl Strong Wildlife Biologist, Don Edwards San Francisco

Bay NWR Tidal marsh ecosystem and waterbird teams

Louis Terrazas Wildlife Refuge Specialist, Antioch Dunes and San Pablo Bay NWRs

Riverine dune ecosystem team

Rachel Tertes Wildlife Biologist, Don Edwards San Francisco Bay NWR

Tidal marsh ecosystem and waterbird teams

Ellen Tong Budget Technician Administrative team Jared Underwood Refuge Manager, Don Edwards San Francisco

Bay NWR Tidal marsh ecosystem, waterbird and human well-being teams

Ed VanTil Maintenance Worker Infrastructure maintenance team

Key: GIS = Geographic Information Systems; NRMP = natural resource management plan.

Notes: All individuals listed in the table are staff of the San Francisco Bay National Wildlife Refuge Complex unless otherwise noted; Region 8 Inventory and Monitoring Program staff are noted with an asterisk The core team is the group of individuals responsible for planning and carrying out the project.

Individuals are listed with their primary teams but may have participated on multiple teams.

2.2 Planning Approach

Development of this NRMP was guided by the Region 8 Methodology for Identifying Priority Resources of Concern (USFWS 2015) and the Open Standards for the Practice of Conservation (Conservation Measures Partnership 2013). How these resources were used is described in the following. Additional planning methods specifically relating to human well-being targets are discussed further in chapter 5.

2.2.1 Identifying Priority Natural Resources of Concern

Refuges support a wide variety of interacting species, communities, and ecosystems. Although conserving all aspects of natural biodiversity is desired, the Service lacks the resources to focus on every element of biodiversity in the Refuge Complex. For this reason, the project team prioritized natural resources of conservation concern that should be a focus of management in the Refuge Complex, referred to as priority ROCs (Service policy 620 FW 1), targets, or conservation targets (the latter is used most frequently in this NRMP).2 Priority ROCs or conservation targets can be species, communities, or ecosystems, and their selection is central to the development of conservation strategies presented in this NRMP and the ability of the Refuge Complex to evaluate conservation progress over time.

The project team followed these 6 generalized steps to identify Refuge Complex conservation targets:

1. Compile refuge species lists and standardize species scientific names to the International

Taxonomic information standard (IT IS; see https://www.itis.gov/).

2. Compile refuge purposes and establishing legislation.

3. Compile larger landscape conservation plans applicable to the refuge(s).

4. Compile lists of sensitive (such as federally threatened and endangered species) and USFWS trust species (such as migratory birds and anadromous fish)

5. Develop and apply species ranking criteria using lists above (2–4) and Refuge Complex elicitation.

6. Review ranking results and identify priority conservation targets. These are high-ranking species (such as federally listed species), communities of high-ranking species (such as waterbirds), or ecosystems (such as a vernal pool grassland ecosystem).

Resulting priority conservation targets (communities or ecosystems) presented in this NRMP have one or more of the following characteristics, including:

identified in refuge purposes or establishing legislation support federally listed threatened or endangered species found in limited areas that overlap a refuge (or refuges) in the Refuge Complex identified as Service trust resources (i.e., migratory birds, anadromous and interjurisdictional fish, marine mammals, federally listed species [601 FW 1.8])

2 These and other terms are defined in appendix A, “Glossary.”

https://www.itis.gov/ identified as a priority natural resource in larger landscape conservation plans indicative/representative of ecological processes or drivers that shape refuge communities/ecosystems or surrounding landscapes support maintenance or restoration of biological integrity, diversity, and environmental health (601 FW 3) provide a direct or indirect benefit to people

The criteria and associated scoring and weights used to calculate species scores and ultimately select Refuge Complex conservation targets are referenced in appendix B.

Additional details about the target general selection process are presented in Methodology for Identifying Priority Resources of Concern (USFWS 2015a).

2.2.2 Planning Process and Timeline

The project team used the Open Standards conservation planning process to support development and to guide implementation of the NRMP. This process promotes an adaptive and evidence-based conservation practices by encouraging the following:

specifying measurable desired results in terms of conservation outcomes, not just actions documenting our assumptions behind management strategies being explicit about how we believe our actions will lead to desired results monitoring outcomes to track conservation progress and test our assumptions regarding how our actions lead to desired results adapting strategies based on what we learn by using data and analyses (evidence) to promote doing more of what works (and less of what does not work) sharing our results and being transparent about what worked and what did not work to advance conservation at a larger landscape scale

Figure 1 shows the five steps composing the Open Standards adaptive management cycle. The NRMP and companion IMP represent steps one and two of the Open Standards process and provide refuge staff with a framework for annual evaluation, learning, and adaptation…