Marine Sanctuaries Conservation Series ONMS-14-09

Ocean Climate Indicators: A Monitoring 

Inventory and Plan for Tracking Climate Change 

in the North-central California Coast and Ocean 

Region

U.S. Department of Commerce

National Oceanic and Atmospheric Administration

National Ocean Service

Office of National Marine Sanctuaries August 2014
About the Marine Sanctuaries Conservation Series

The Office of National Marine Sanctuaries, part of the National Oceanic and 

Atmospheric Administration, serves as the trustee for a system of 14 marine protected 

areas encompassing more than 170,000 square miles of ocean and Great Lakes waters. 

The 13 national marine sanctuaries and one marine national monument within the 

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Because of considerable differences in settings, resources, and threats, each marine 

sanctuary has a tailored management plan. Conservation, education, research, 

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are available on the Office of National Marine Sanctuaries Web site 

(http://www.sanctuaries.noaa.gov).
Ocean Climate Indicators: A Monitoring Inventory and Plan 

for Tracking Climate Change in the North-central California 

Coast and Ocean Region

Duncan, B.E., K.D. Higgason, T.H. Suchanek, J. Largier, J. Stachowicz, S. Allen, S. 

Bograd, R. Breen, H. Gellerman, T. Hill, J. Jahncke, R. Johnson, S. Lonhart, S. Morgan, 

J. Roletto, F. Wilkerson.

A Working Group of the Gulf of the Farallones National Marine Sanctuary Advisory 

Council 

Silver Spring, Maryland

August 2014

U.S. Department of Commerce

Penny Pritzker, Acting Secretary

National Oceanic and Atmospheric Administration

Kathryn Sullivan, Ph.D.

Acting Under Secretary of Commerce for Oceans and Atmosphere

National Ocean Service

Holly Bamford, Ph.D., Assistant Administrator

Office of National Marine Sanctuaries

Daniel J. Basta, Director
Disclaimer

Report content does not necessarily reflect the views and policies of the Office of 

National Marine Sanctuaries or the National Oceanic and Atmospheric Administration, 

nor does the mention of trade names or commercial products constitute endorsement or 

recommendation for use.

Report Availability

Electronic copies of this report may be downloaded from the Office of National Marine 

Sanctuaries web site at http://sanctuaries.noaa.gov.

Cover

(left) Shoreline along North-central California coast; (middle): Brandt’s cormorant; 

(right, top to bottom): San Francisco tide gauge; Bull kelp; Gopher rockfish.

Suggested Citation

Duncan, B.E., K.D. Higgason, T.H. Suchanek, J. Largier, J. Stachowicz, S. Allen, S. 

Bograd, R. Breen, H. Gellerman, T. Hill, J. Jahncke, R. Johnson, S. Lonhart, S. Morgan, 

J. Roletto, F. Wilkerson. 2014. Ocean Climate Indicators: A Monitoring Inventory and 

Plan for Tracking Climate Change in the North-central California Coast and Ocean 

Region. Report of a Working Group of the Gulf of the Farallones National Marine 

Sanctuary Advisory Council. Marine Sanctuaries Conservation Series ONMS-14-09. 

U.S. Department of Commerce, National Oceanic and Atmospheric Administration, 

Office of National Marine Sanctuaries, Silver Spring, MD. 81pp.

Contact

Kelley Higgason, Ocean Climate Initiate Coordinator, Gulf of the Farallones National 

Marine Sanctuary: kelley.higgason@noaa.gov.
Working Group Members

Sarah Allen - National Park Service

Steven Bograd - NMFS Southwest Fisheries Science Center

Bob Breen - Friends of Fitzgerald Marine Reserve; GFNMS Sanctuary Advisory Council (SAC)

Holly Gellerman - California Department of Fish and Wildlife

Tessa Hill - University of California (UC) Davis, Bodega Marine Laboratory

Jaime Jahncke (Working Group Chair) – Point Blue Conservation Science; GFNMS SAC

Rebecca Johnson - California Academy of Sciences; GFNMS

John Largier - UC Davis, Bodega Marine Laboratory; GFNMS SAC

Steve Lonhart - Monterey Bay National Marine Sanctuary

Steven Morgan - UC Davis, Bodega Marine Laboratory

Jay Stachowicz - UC Davis

Tom Suchanek - USGS Western Ecological Research Center; UC Davis

Frances Wilkerson - San Francisco State University, Romberg Tiburon Center

Staff to Working Group

Benét Duncan (Facilitator and Project Lead) – Gulf of the Farallones National Marine 

Sanctuary/University Corporation for Atmospheric Research

Kelley Higgason - Gulf of the Farallones National Marine Sanctuary

Jan Roletto - Gulf of the Farallones National Marine Sanctuary

Sanctuary Superintendents

Maria Brown – Gulf of the Farallones National Marine Sanctuary

Dan Howard – Cordell Bank National Marine Sanctuary

Contributors

Abe Doherty – California Ocean Protection Council

Sarah Flores – California Ocean Protection Council

Matt Gerhart – California State Coastal Conservancy

Jennifer Patterson – Central and Northern California Ocean Observing System (CeNCOOS)

Project Mentors

Kelley Higgason (Lead Mentor) - Gulf of the Farallones National Marine Sanctuary

Tom Suchanek (Lead Mentor) - USGS Western Ecological Research Center; UC Davis

Dan Cayan –USGS National Research Center, Western Region; Scripps Institution of 

Oceanography

John Largier – UC Davis, Bodega Marine Laboratory

Jay Stachowicz – UC Davis

i
Abstract

The impacts of climate change have been observed both globally and on regional scales, such as

in the North-central California coast and ocean, a region that extends from Point Arena to Point 

Año Nuevo and includes the Pacific coastline of the San Francisco Bay Area. Because of the 

high economic and ecological value of the region’s marine environment, Gulf of the Farallones 

National Marine Sanctuary (GFNMS) and other agencies and organizations have recognized the 

need to evaluate and plan for climate change impacts. 

Climate change indicators provide information about the presence and potential impacts of 

climate change. While climate change indicators exist for the nation and for the state of 

California as a whole, no system of ocean climate indicators exist that specifically consider the 

unique characteristics of the North-central California coast and ocean region. To that end, 

GFNMS collaborated with over 50 federal, state, and regional natural resource managers, 

research scientists, and other partners to develop a set of eight physical and four biological ocean 

climate indicators specific to this region. 

A smaller working group of regional experts developed overarching indicator monitoring 

recommendations, and specific metrics and monitoring goals, objectives, strategies, and activities 

for each of the twelve ocean climate indicators. Broadly speaking, these strategies are centered 

on maintaining existing indicator monitoring, and expanding or establishing new monitoring in 

critical habitats. To maximize the utility of these indicators for decision-makers, priority levels, 

current and potential future partners, funding requirements, and implementation timelines are 

provided for each indicator monitoring strategy. 

Key Words

Climate change, ocean climate, indicator, Gulf of the Farallones National Marine Sanctuary, 

GFNMS, climate impact, fishes, seabirds, sensitive species, primary productivity, sea level, sea 

surface temperature, ocean acidification, dissolved oxygen, salinity, air temperature

ii
Acknowledgements

The authors would like to thank the University Corporation for Atmospheric Research (UCAR) 

and NOAA’s Climate Program Office for their financial support toward the Ocean Climate 

Indicators project, including the development of this document. This work was completed as part 

of UCAR’s Postdocs Applying Climate Expertise (PACE) postdoctoral fellowship program, 

hosted by NOAA Gulf of the Farallones National Marine Sanctuary (GFNMS) and US 

Geological Survey (USGS) Western Ecological Research Center (WERC). Support was also 

provided by the California Ocean Science Trust (OST) and the US Fish and Wildlife Service’s 

California Landscape Conservation Cooperative (CA LCC). The authors would also like to thank 

Andrew Gunther, Bay Area Ecosystems Climate Change Consortium and Josh Adams, USGS 

Western Ecological Research Center, for their thorough and thoughtful reviews of this report, as 

well as all of the individuals, agencies, organizations, and institutions that provided numerous inkind staff hours toward the completion of this document.

iii
Table of Contents

Topic Page

Working Group Members................................................................................................................ i

Staff to Working Group ................................................................................................................... i

Sanctuary Superintendents............................................................................................................... i

Contributors..................................................................................................................................... i

Project Mentors................................................................................................................................ i

Abstract........................................................................................................................................... ii

Key Words...................................................................................................................................... ii

Acknowledgements........................................................................................................................iii

Table of Contents........................................................................................................................... iv

List of Figures and Tables.............................................................................................................. vi

Executive Summary........................................................................................................................ 8

Physical Indicators...................................................................................................................... 8

Biological Indicators................................................................................................................... 8

Regional Ocean Climate Indicators Monitoring Goal and Objectives ....................................... 9

Indicators Monitoring Strategies and Activities......................................................................... 9

Additional Content.................................................................................................................... 10

Introduction................................................................................................................................... 11

Climate Change in the North-central California Coast and Ocean Region .............................. 11

Ocean Climate Indicators.......................................................................................................... 12

Ocean Climate Indicators Project Overview............................................................................. 14

Ocean Climate Indicators Monitoring Goal and Objectives..................................................... 16

Monitoring Inventory and Plan Overview ................................................................................ 16

Study Region............................................................................................................................. 18

Ocean Climate Indicators Monitoring Strategies: Physical.......................................................... 21

Physical Indicator #1: Air Temperature.................................................................................... 21

Physical Indicator #2: Alongshore Wind Speed and Direction ................................................ 25

Physical Indicator #3: Sea Surface Temperature ...................................................................... 28

Physical Indicator #4: Sea Surface Salinity.............................................................................. 33

Physical Indicator #5: Dissolved Oxygen................................................................................. 36

Physical Indicator #6: Ocean Chemistry................................................................................... 38

Physical Indicator #7: Wave Height and Direction .................................................................. 40

Physical Indicator #8: Sea Level............................................................................................... 43

Ocean Climate Indicators Monitoring Strategies: Biological....................................................... 46

Biological Indicator #1: Primary Productivity.......................................................................... 46

Biological Indicator #2: Mid-Trophic Level Species Abundance, Biomass, & Phenology ..... 49

Biological Indicator #3: Spatial Extent of Habitat-Forming Organisms.................................. 54

Biological Indicator #4: Seabird Phenology, Productivity, & Diet .......................................... 57

Summary and Conclusion............................................................................................................. 63

Literature Cited ............................................................................................................................. 65

List of Acronyms .......................................................................................................................... 67

Report Photo and Figure Credits................................................................................................... 69

Appendix A: Climate Change Priority Management Questions................................................... 70

iv
Appendix B: Indicator Selection Criteria & Post-Assessment Questions.................................... 71

Appendix C: Gulf of the Farallones Regional Ecosystem Description ........................................ 72

General Overview ..................................................................................................................... 72

Habitat #1: Sandy Beaches ....................................................................................................... 73

Habitat #2: Rocky Intertidal (aka Rocky Shore)....................................................................... 73

Habitat #3: Nearshore Subtidal (aka Shallow Subtidal) ........................................................... 74

Habitat #4: Estuaries and Bays................................................................................................. 75

Habitat #5: Islands .................................................................................................................... 76

Habitat #6: Offshore ................................................................................................................. 76

Appendix D: Conceptual Ecological Model for North-central California Coast and Ocean ....... 79

Appendix E: Priority Levels of Indicator Monitoring Strategies.................................................. 80

Appendix F: Promising Mid-Trophic Level Species.................................................................... 81

v
List of Figures and Tables

Figure/Table Number and Title Page

Figure 1. Scientist Sampling Phytoplankton................................................................................... 8

Figure 2. Brandt’s Cormorant......................................................................................................... 8

Figure 3. Map of study region (thick red lines), with related sanctuary boundaries (black solid 

lines) and proposed sanctuary expansion areas(black dashed lines) .............................................. 9

Figure 4. Shoreline along North-central California coast............................................................. 10

Figure 5. Physical ocean climate indicators for the North-central California coast and ocean 

region ............................................................................................................................................ 12

Figure 9. Annual maximum air temperature at Southeast Farallon Island from 1971 – 2012. The 

diagonal black line illustrates a linear regression indicating the trend in the data (Point Blue 

Conservation Science, unpublished data). .................................................................................... 21

Figure 10. Giant Green Anemone................................................................................................ 49

Figure 11. California Mussels....................................................................................................... 54

Figure 12. Seagrass bed along North-central California coast ..................................................... 55

Figure 13. Brandt’s Cormorant..................................................................................................... 58

Figure 14. Common Murre ........................................................................................................... 58

Table 1. Monitoring Plan Symbols............................................................................................... 18

Table 2. Monitoring strategies and activities for air temperature................................................. 22

Table 3. Existing monitoring data sources for air temperature..................................................... 23

Table 4. Monitoring strategies and activities for wind speed and direction ................................. 26

Table 5. Existing monitoring data sources for wind speed and direction..................................... 26

Table 6. Monitoring strategies and activities for SST .................................................................. 28

Table 7. Existing monitoring data sources for SST...................................................................... 30

Table 8. Monitoring strategies and activities for SSS................................................................... 34

Table 9. Existing monitoring data sources for SSS ...................................................................... 35

Table 10. Monitoring strategies and activities for DO ................................................................. 36

Table 11. Existing monitoring data sources for DO ..................................................................... 37

Table 12. Monitoring strategies and activities for ocean chemistry ............................................. 39

Table 13. Existing monitoring data sources for ocean chemistry................................................. 40

Table 14. Monitoring strategies and activities for wave height and direction.............................. 41

Table 15. Existing monitoring data sources for wave height and direction.................................. 42

Table 16. Monitoring strategies and activities for sea level ......................................................... 44

Table 17. Existing monitoring data sources for sea level ............................................................. 45

Table 18. Monitoring strategies and activities for primary productivity...................................... 46

Table 19. Existing monitoring data sources for primary productivity.......................................... 48

Table 20. Selected mid-trophic level species by habitat type....................................................... 50

Table 21. Monitoring strategies and activities for mid-trophic species........................................ 51

Table 22. Existing monitoring data sources for selected mid-trophic species.............................. 52

Table 23. Selected habitat-forming organisms by habitat type..................................................... 55

Table 24. Monitoring strategies and activities for habitat-forming organisms............................. 56

Table 25. Existing monitoring data sources for selected habitat-forming organisms................... 57

vi
Table 26. Selected seabird species by habitat type ....................................................................... 58

Table 27. Monitoring strategies and activities for seabirds.......................................................... 59

Table 28. Existing monitoring data sources for selected seabird species..................................... 61

vii
Executive Summary

The impacts of climate change, defined as increasing atmospheric and oceanic carbon dioxide and 

associated increases in average global temperature and oceanic acidity, have been observed both 

globally and on regional scales, such as in the North-central California coast and ocean, a region 

that extends from Point Arena to Point Año Nuevo and includes the Pacific coastline of the San 

Francisco Bay Area. Because of the high economic and ecological value of the region’s marine 

environment, the Gulf of the Farallones National Marine Sanctuary (GFNMS) and other agencies 

and organizations have recognized the need to evaluate and plan for climate change impacts. 

Climate change indicators can be developed on global, regional, and site-specific spatial scales and 

they provide information about the presence and potential impacts of climate change. While 

indicators exist for the nation and for the state of California as a whole, no system of ocean climate 

indicators exist that specifically consider the unique characteristics of the California coast and ocean 

region. To that end, GFNMS collaborated with over 50 regional, federal, and state natural resource 

managers, research scientists, and other partners to develop a set of ocean climate indicators 

specific to this region. A smaller working group of 13 regional partners developed monitoring 

goals, objectives, strategies, and activities for the indicators and recommended selected species for 

biological indicators, resulting in the Ocean Climate Indicators Monitoring Inventory and Plan. The 

working group considered current knowledge of ongoing monitoring, feasibility of monitoring, 

costs, and logistics in selecting monitoring activities and selected species.

Physical Indicators

The physical ocean climate indicators include:

• Ocean Water Properties

o Sea Surface Temperature

o Dissolved Oxygen

o Sea Surface Salinity

o Ocean Chemistry (pH)

• Sea Level

• Wave Height & Direction

• Atmospheric Properties 

o Air Temperature

o Alongshore Wind Speed

Biological Indicators

The biological ocean climate indicators include:

• Primary Productivity

• Abundance, Biomass, & Phenology of 

 Mid-Trophic Level Species

• Spatial Extent of Habitat-Forming Organisms 

• Phenology, Productivity, & Diet of Seabirds 

Figure 1. Scientist Sampling 

Phytoplankton

Figure 2. Brandt’s Cormorant

8
Regional Ocean Climate Indicators 

Monitoring Goal and Objectives

Monitoring Goal:

Promote comprehensive and coordinated 

management of marine resources by 

increasing understanding of the ecological 

impacts of climate change on the Northcentral California coast and ocean region, 

through the monitoring and evaluation of 

physical and biological ocean climate 

indicators.

Objectives to Meet the Monitoring Goal:

1. Determine the status and trends of 

ocean climate indicators along the 

North-central California coast and 

ocean region through existing 

monitoring programs and by identifying 

needs and opportunities for new or 

expanded monitoring efforts.

2. Assess the vulnerability of specific 

geographic areas, ecosystems, and 

ecosystem components within the 

North-central California coast and 

ocean region to the impacts of climate 

change.

Indicators Monitoring Strategies and Activities

The Indicators Working Group identified several overarching indicator monitoring 

recommendations:

1. Continued and/or expanded financial support for ongoing indicator monitoring is vital for 

science-based climate change decision-making because it allows for identification of longterm, climate-scale changes in the region’s ecosystems.

2. Expanded or new indicator monitoring would provide important information for natural 

resource managers.

3. Synthesis of existing regional climate change research is key to ensuring that monitoring is 

as efficient and useful as possible.

4. There is a need for increased communications with regional and local government agencies 

to ensure that natural resource managers have access to the information, partners, and 

resources that they need to assess and reduce their vulnerability to climate change.

Figure 3. Map of study region (thick red lines), with related 

sanctuary boundaries (black solid lines) and proposed 

sanctuary expansion areas(black dashed lines)

9
Additional Content

The Indicators Monitoring Inventory and Plan also 

contains the following for each ocean climate 

indicator:

• An inventory of the best available current 

and historical monitoring 

• Unique monitoring strategies and activities 

• Case studies to provide specific examples of 

the indicators’ utility in a decision-making 

context

Figure 4. Shoreline along North-central California coast

10
Introduction

Climate Change in the North-central California Coast and Ocean Region

The waters along the North-central California coast are part of one of the world’s major coastal 

upwelling systems (Bakun 1973; Chavez 2009). Extensive fisheries, tourism, and recreation play a 

significant role in the region’s economy (SFEP 2011). The importance of the rich marine ecosystem 

from Point Arena to Point Año Nuevo has been recognized by the establishment of contiguous 

national marine sanctuaries by the National Oceanic and Atmospheric Administration (NOAA) and 

their proposed expansions. Adjacent to the major metropolitan area surrounding San Francisco Bay 

and encompassing the outflow of California’s major river system, the national marine sanctuaries 

(NMS) included in the study region are Gulf of the Farallones (GFNMS), Cordell Bank (CBNMS), 

and the northern portion of Monterey Bay (MBNMS). 

Climate Change Impacts:

The impacts of climate change are already being observed in the North-central California coast and 

ocean region. In 2010, a working group of the GFNMS and CBNMS Sanctuary Advisory Councils 

(SAC) authored a report, "Climate Change Impacts: Gulf of the Farallones and Cordell Bank 

National Marine Sanctuaries," highlighting recent climate change observations and potential threats 

to the region, including (Largier et al. 2010): 

• Observed increase in air temperature at the South Farallon Islands from 1971 – 2007; 

• Observed increase in sea level at the mouth of the San Francisco Bay, by 20cm over the last 

100 years; 

• Observed increase in frequency and strength of extreme weather events, including North 

Pacific cyclones; 

• Observed increase in the northerly winds that drive coastal upwelling of cold, nutrient-rich 

waters;

• Observed northward shift of key species including Humboldt squid (Dosidicus gigas), 

volcano barnacle (Tetraclita rubescens), and bottlenose dolphins (Tursiops truncatus);

• Projected increase in global sea level of 40-75cm by 2050 relative to the sea level in 1990;

• Projected decrease in regional seawater pH due to uptake of carbon dioxide by the ocean; 

and

• Potential for effects of climate change to be compounded by parallel environmental changes 

associated with local human activities.

Parallel Ecosystem Stressors:

Additional stressors can act in parallel to anthropogenic climate change to impact the health of 

North-central California marine ecosystems. These stressors include natural regional-scale climate 

variability and human activities such as land development, commercial fishing and mariculture, 

recreation, and water pollution (GFNMS 2010; Largier et al. 2010; SFEP 2011). Regional and 

global-scale natural climate variability that has been shown to impact the study region includes the 

El Niño Southern Oscillation (ENSO), the Pacific Decadal Oscillation (PDO), and the North Pacific 

Gyre Oscillation (NPGO) (Largier et al. 2010), each of which results in changes to wind patterns, 

ocean circulation, water temperatures, sea level, storminess, and the extent of coastal fog in the 

region. 

These parallel ecosystem stressors can interact with the effects of anthropogenic climate change to 

impact the region in new and varied ways. For example, shoreline species whose habitat ranges are 

already being reduced due to climate change-induced sea level rise may be limited in their ability to 

11
migrate shoreward due to land development. Depending on their phase, natural climate variability 

such as ENSO and the PDO may further exacerbate or reduce sea level rise, thus intensifying or 

reducing the stress that a particular species may be experiencing. 

Regional natural resource managers can act to help ecological systems adapt to climate change and 

increase ecosystem resilience (ability to resist, recover, or rebound), by reducing non-climate 

stressors on vulnerable habitats and species. This report and the project as a whole are designed to 

identify ocean climate indicators that will help managers and researchers track the impacts of 

climate change on the region and identify habitats and species that are particularly vulnerable. Case 

studies provide examples of actions that managers can take based on the status and trends of these 

indicators. This report also provides collaboratively-developed ocean climate indicator monitoring 

goals, objectives, and activities to better understand the impacts of climate change on the Northcentral California coast and ocean region.

Ocean Climate Indicators

Ocean climate indicators are measurements that provide information about the presence and impacts 

of climate change in a region. They can be divided into two categories: biological indicators, which 

enable monitoring of the biological response of an ecosystem to climate change, and physical 

indicators, which enable monitoring of changes in the physical environment of an ecosystem to 

climate change. Examples of biological ocean climate indicators include the abundance of a 

particular seabird species or the extent of biogenic habitat, such as seagrass, kelp, or mussel beds. 

Physical ocean climate indicators can include sea level, sea surface temperature, or the pH of ocean 

waters. Ocean climate indicators have been used by research scientists and decision-makers for a 

range of spatial scales, including 

individual estuaries in the U.S. 

Environmental Protection Agency’s 

Climate Ready Estuaries program; 

the State of California; the United 

States; and globally by such 

agencies as the National Oceanic 

and Atmospheric Administration 

(NOAA) and the National 

Aeronautics and Space 

Administration (NASA). Whereas 

locally-scaled indicators can 

provide insights about important 

ecosystem changes and processes 

that might be omitted by globallyscaled indicators, global indicators 

can provide a broad perspective on 

climate change impacts.

The GFNMS Ocean Climate 

Initiative and numerous other local, 

state, and federal agencies, nonprofit organizations, and academic 

institutions need a clear way to Figure 5. Biological ocean climate indicators for the North-central 

California coast and ocean region

12
understand and communicate the 

presence and impacts of climate 

change within the North-central 

California coast and ocean region. 

To help meet this need, a set of 

physical and biological ocean 

climate indicators was 

collaboratively developed for the 

region from Point Año Nuevo to 

Bodega Head (Figures 1 and 2). 

The region of focus was expanded 

northward to Point Arena because 

of the consistency among the 

habitats, ecosystems, and climate 

forcings in the region. The 

indicators may also be more 

broadly informative north and south 

of the study area. The indicators 

are, to GFNMS’ knowledge, the 

first system of ocean climate 

indicators developed specifically 

for the North-central California 

coast and ocean region and the first

in the National Marine Sanctuary

System, representing the consensus of over 50 regional research scientists, natural resource 

managers, and decision-makers. 

Details about how these indicators were selected follow in the Ocean Climate Indicators Project 

overview, and in Appendices A-F. Throughout the indicators development process, emphasis was 

placed on identifying those physical and biological indicators that had a clear connection to 

anthropogenic climate change and long pre-existing monitoring programs to allow for identification 

of climate-scale changes in the study region. The indicators contained in this report provide a clear 

and concise way of communicating to decision-makers the status and trends of important physical 

factors of the climate system, and potential concomitant changes in biological/ecological parameters 

of the North-central California coast and ocean region associated with those factors. Maintaining 

ongoing and recommended future monitoring to evaluate changes in these factors over time will 

enable natural resource managers and decision-makers to better evaluate their own unique natural 

resources in order to inform and improve their management strategies.

For example, indicators such as sea level or sea surface temperature can help with the identification 

of coastal and marine habitats and species that are particularly vulnerable to the impacts of climate 

change. These habitats and species can be protected from non-climate stressors to increase their 

resiliency to climate change.

Research scientists can also use these indicators to assess the status and impacts of climate change 

in the North-central California coast and ocean region. The indicator monitoring opportunities 

identified in this report hopefully also will lead to new or expanded monitoring that is of high utility 

to both research scientists and natural resource managers. 

Figure 6. Physical ocean climate indicators for the North-central 

California coast and ocean region

13
Ocean Climate Indicators Project Overview

The Ocean Climate Indicators project leverages existing relationships between the GFNMS Ocean 

Climate Initiative and federal, state, local agencies, universities, and NGOs to collaboratively 

develop a set of physical and biological ocean climate indicators for the North-central California 

coast and ocean region. Funded by NOAA and the University Corporation for Atmospheric 

Research (UCAR) as part of the Postdocs Applying Climate Expertise (PACE) Fellowship Program, 

the Ocean Climate Indicators project is the first ocean climate indicators development project by 

National Marine Sanctuary staff. Advisors for the Ocean Climate Indicators project include the 

Ocean Climate Initiative Coordinator at GFNMS and research scientists from the US Geological 

Survey (USGS), the University of California Davis, and Scripps Institution of Oceanography, with 

additional consultation provided by Point Blue Conservation Science (formerly PRBO Conservation 

Science). Collaborating scientists and managers are from 26 institutions, NGOs, and agencies that 

include the California Academy of Sciences, University of California (UC) Berkeley, UC Davis, 

and UC Santa Cruz; San Francisco State University; San Francisco Bay Joint Venture; California 

Department of Fish and Wildlife (CDFW); California Coastal Commission; California Coastal 

Conservancy; California Ocean Protection Council; National Park Service (NPS); US Fish and 

Wildlife Service (USFWS); National Weather Service (NWS); and National Marine Fisheries 

Service (NMFS). 

The indicator development process used in the Ocean Climate Indicators project is grounded in the 

National Research Council publication, “Ecological Indicators for the Nation” (NRC 2000) and 

detailed in the project flowchart (Figure 3). In the first phase of the Ocean Climate Indicators 

project, an extensive review of peer-reviewed climate change literature for the North-central 

California coast and ocean region laid the groundwork for all of the work that followed. 

Concurrently, GFNMS staff collaborated to develop a set of priority management questions 

(Appendix A) that the indicators should help to address. Following discussions with project mentors 

and other partners, the indicator selection criteria used by the National Research Council (NRC 

2000) were modified to create selection criteria appropriate to the North-central California coast and 

ocean region and that addressed core needs of regional natural resource managers (Appendix B). 

These selection criteria were specifically developed to ensure that each indicator chosen was 

scientifically and statistically sound, and that it helped to address the priority management 

questions. A specific emphasis was placed on identifying indicators with a clear link to climate 

change, and with long-term datasets to allow for statistically sound analysis of the impacts of 

climate change on the region. An Ecosystem Description (Appendix C) was written to identify the 

six major habitat types in the North-central California coast and ocean region, key flora and fauna in 

each habitat, and vulnerabilities of each habitat to climate change. These key components were 

mapped onto a Conceptual Ecological Model (Appendix D) to further emphasize the processes by 

which climate change can impact the region.

14
Figure 7. Ocean Climate Indicators Project Flowchart

Phase II of the Ocean Climate Indicators project was focused on determining the indicators 

themselves. The extensive literature review and the Ecosystem Description from Phase I informed 

the creation of a large set of candidate ocean climate indicators. These indicators were initially 

refined to a smaller set of 10 physical and 13 biological ocean climate indicators by the project 

mentors. These indicators were then assessed by 51 of 76 invited partner scientists and managers 

via an Indicator Survey, which contained a series of questions to assess how well each indicator met 

the indicator selection criteria (Appendix B) and allowed respondents to suggest additional 

indicators. All Indicator Survey respondents were invited to provide additional input at an Ocean 

Climate Indicators Workshop on August 28, 2012, and 36 of them attended. Each of four breakout 

groups at the workshop recommended a set of priority indicators for further analysis. Indicators that 

were recommended by at least three breakout groups were taken to be broadly recommended, and 

were ultimately selected to be the final set of ocean climate indicators for the North-central 

California coast and ocean region (Figures 1 and 2). A full summary of the Ocean Climate 

Indicators Workshop is available online, at http://farallones.noaa.gov/manage/climate/ 

indicators.html.

There is consensus among regional research scientists and managers that these indicators provide 

important information about the status and trends of physical and biological components of the 

North-central California coast and ocean region. The recommended biological indicators are 

15
distributed across trophic levels to provide an assessment of the impacts of climate change on key 

biota in the region (Figure 2). For example, primary producers represent the base of the food web, 

and changes in the presence of photosynthetic organisms like phytoplankton can cascade up through 

trophic levels to impact mid-trophic level species like macroinvertebrates and higher trophic level 

seabirds like common murres, Cassin’s auklets, and Brandt’s cormorants. There are many possible 

indicators and species that could be chosen, especially for biological indicators. In addition to 

providing relevant information about current and potential future impacts of climate change on the 

region, the chosen indicators either already have legacy data, or data can be obtained relatively 

easily. 

Phases III and IV of the Ocean Climate Indicators Project were focused on developing detailed 

documentation about the indicators and their development, including the Indicators Monitoring 

Inventory and Plan. A working group of 13 regional research scientists and natural resource 

managers, many of whom participated in the Indicator Selection Workshop, was approved by the 

GFNMS Sanctuary Advisory Council to develop this Indicators Monitoring Inventory and Plan. 

Each member of this interdisciplinary working group had expertise in at least one of the ocean 

climate indicators, and together, the group worked to maximize the utility of this inventory and plan 

for both natural resource managers and research scientists. 

The working group was convened in a series of five meetings from April – November 2013. At the 

first Indicators Working Group meeting, attendees approved the indicators monitoring goals and 

objectives and then formed breakout groups to provide detailed monitoring strategies and activities 

for each indicator. The working group then provided revisions and final approval of this monitoring 

inventory and plan at subsequent meetings. A subgroup of working group four members 

volunteered to identify “selected species” for each of the biological indicators (Figure 2). For these 

selected species, there is a clear, scientifically accepted mechanism by which climate change can 

alter their distribution or abundance, and monitoring is already available in some portions of the 

study region.

Ocean Climate Indicators Monitoring Goal and Objectives

Monitoring Goal:

Promote comprehensive and coordinated management of marine resources by increasing 

understanding of the ecological impacts of climate change on the North-central California coast and 

ocean region, through the monitoring and evaluation of physical and biological ocean climate 

indicators.

Objectives to Meet the Monitoring Goal:

1. Determine the status and trends of ocean climate indicators along the North-central 

California coast and ocean region through existing monitoring programs and by identifying 

needs and opportunities for new or expanded monitoring efforts.

2. Assess the vulnerability of specific geographic areas, ecosystems, and ecosystem 

components within the North-central California coast and ocean region to the impacts of 

climate change.

Monitoring Inventory and Plan Overview

A working group consisting of 13 regional natural resource managers and research scientists, three 

GFNMS staff members who provided technical support, and the GFNMS and CBNMS 

Superintendents helped to develop the Ocean Climate Indicators Monitoring Inventory and Plan. In 

16
the pages that follow, for each indicator, monitoring strategies and activities are given; the best 

available monitoring data are identified; opportunities for improving or expanding existing 

monitoring or for establishing new indicator monitoring are detailed; and case studies provide 

specific examples of the indicators’ utility in a decision-making context. 

It should be noted that the Ocean Climate Indicators Monitoring Inventory and Plan is not intended 

to serve as a mandate for the research and management communities. Rather, it is a guide for 

existing and potential future monitoring of ocean climate indicators that represents the consensus of 

leading regional research scientists and natural resource managers from a range of universities, nongovernmental organizations (NGOs), and state and federal government agencies. Long-term 

monitoring is essential for ensuring that the ecosystem is well understood, observing the impacts of 

climate change on the region, and identifying habitats that may be particularly vulnerable in the 

future. Currently, funding is provided for many valuable indicator monitoring projects on a year-toyear basis only.

Key purposes of this document are to:

1. Increase support for long-term monitoring of ocean climate indicators as a high funding 

priority. 

2. Promote expanded and new monitoring of ocean climate indicators that would provide 

valuable information for natural resource managers.

3. Increase support for the synthesis of existing research about the regional impacts of changes 

in the ocean climate indicators.

4. Promote increased communications with government agencies to ensure that natural 

resource managers have access to the information, partners, and resources that they need to 

assess vulnerability.

Following approval by the GFNMS SAC, the Ocean Climate Indicators Monitoring Inventory and 

Plan was forwarded to GFNMS sanctuary management to consider how to integrate the report’s 

recommendations into the GFNMS Management Plan and program areas of Research and 

Monitoring, Ecosystem Protection, and Education and Outreach.

The monitoring strategies and activities are presented in separate tables for each indicator, along 

with information about each activity’s priority level, current and potential partners, funding 

requirements, and implementation timelines. Indicator monitoring activities with “critical” priority 

levels have the potential to provide the long time series necessary to better understand climate 

change impacts on the region, and can capture more critical information about climate change 

impacts more efficiently than “very important” and “important” priority activities. While all 

indicator monitoring activities were carefully selected and continued funding for these activities is 

important, “critical” priority activities are those for which funding is critical, even during times of 

limited financial resources. We note that continued funding for some indicators is uncertain. To 

facilitate increased ease of use, all “critical” monitoring activities are compiled in Appendix E. For 

consistency, the symbols presented in Table 1 are used to describe the priority level and funding 

requirements in the tables throughout the document:

17
Table 1. Monitoring Plan Symbols

PRIORITY LEVEL SYMBOLS:

Support for this indicator 

monitoring activity is critical, 

even during times of limited 

financial resources

Support for this indicator 

monitoring activity is very 

important, even during times 

of limited financial resources

Support for this indicator 

monitoring activity is 

important, even during times 

of limited financial resources

NEED FOR ADDITIONAL FUNDING & INFRASTRUCTURE SYMBOLS:

$$$ $$ $

No existing monitoring 

infrastructure or equipment

Some existing monitoring 

infrastructure or equipment

Extensive monitoring 

infrastructure or equipment 

exists

The working group recommends that the Ocean Climate Indicators Monitoring Inventory and Plan 

be updated by GFNMS in two ways:

1. On an annual basis, GFNMS staff should consider updating data sources for each indicator.

2. Every 5 years, the GFNMS SAC should consider convening a working group to review the 

indicators contained in this report, to re-evaluate their utility to managers and their ongoing 

scientific relevance, and to consider adding any new indicators that reflect advances in 

scientific understanding of climate change in the North-central California coast and ocean 

region.

Study Region

The California coast is part of the California Current Ecosystem (CCE), which stretches along the 

west coast of North America from the northern border of the United States to Baja California. The 

CCE is one of only four Eastern Boundary Upwelling Ecosystems in the world (Chavez and Messie 

2009 and references therein), which are characterized by extremely high biological productivity 

(e.g., Bakun 1973; Bakun et al. 2010). This productivity is a result of “upwelling,” a process that 

occurs when equator-ward winds combine with the rotation of the Earth to cause offshore transport 

of coastal surface waters. This surface water is replaced by deeper, colder, more nutrient-rich 

upwelled water. Nutrients fuel the growth and proliferation of phytoplankton in this upwelled water 

as they are exposed to sunlight near the surface. As a result of the increased concentrations of 

phytoplankton that form the base of the food chain, there is increased biological productivity 

throughout the trophic levels, from zooplankton to fish and top predators (Chavez and Messie 2009; 

Bakun et al. 2010). 

The most intense and persistent upwelling in the North-central California coast and ocean region 

generally occurs from March through July (Garcia-Reyes and Largier 2010 and references therein) 

when the atmospheric North Pacific High shifts northward. During relaxation periods in the 

upwelling season, and during the fall transition season, the prevailing equator-ward winds weaken, 

sometimes causing ocean currents to flow to the north and halting upwelling. 

There are six major habitat types in the North-central California coast and ocean region, from Point 

Año Nuevo to Point Arena (Figure 8): sandy beaches, rocky intertidal, nearshore subtidal, estuaries 

and bays, islands, and offshore.

18
Sandy beaches can generally be found along the coastal border of the region, and they are often 

accessible to and used by humans. This habitat type constantly changes due to the influence of 

waves, wind, and tides on sediment transport and inundation time (GFNMS 2008). It is home to 

wrack consumers and invertebrate communities, and breeding and nesting grounds for some 

shorebirds (GFNMS 2010). Sandy beaches are also used by smelt and other fish species for 

spawning and by pinnipeds, including elephant seals and harbor seals, to pup and raise their young 

(Largier et al. 2010).

Rocky intertidal habitat consists 

of rocky areas found between 

high and low tide water levels, 

including, but not limited to, 

portions of Duxbury Reef, the 

Fitzgerald Marine Reserve, the 

Farallon Islands, Bodega Head, 

and the Marin Headlands 

(GFNMS 2008 and 2010; 

Largier et al. 2010). The 

conditions found in this habitat 

type change frequently due to 

tidal inundation and wave 

exposure (GFNMS 2008). These 

changing conditions lead to 

drying and heating/cooling 

during low tide and inundation 

and cooling during high tide 

(GFNMS 2010). Rocky intertidal 

habitat is used by organisms that 

include all trophic levels, from 

habitat-building coralline algae 

to marine invertebrates like 

barnacles, limpets, abalone, 

mussels, sea anemones, and sea 

urchins, to a number of fish 

species, shorebirds, and 

pinnipeds (GFNMS 2008 and 

2010).

Nearshore subtidal habitat lies 

below the low tide line to depths 

of up to 30m, with a seafloor that can be sandy shelf or rocky reef. This habitat is strongly affected 

by upwelling during spring and summer months, and by runoff and precipitation during the winter 

storm season. Shallow depths allow for good light penetration, which allows for high productivity 

of benthic algae on hard substrata. For example, kelp forests provide nursery grounds for fish and 

invertebrates. North of Bodega Head, nearshore subtidal habitat is home to fish species like blue 

rockfish and perch, which in turn provide a food source for other fishes, seabirds, and marine 

mammals (GFNMS 2008 and 2010). 

Figure 8. Map of study region (thick red lines), with related sanctuary 

boundaries (black solid lines) and proposed sanctuary expansion areas 

(black dashed lines)

19
Estuaries and bays in the study region are mostly small and sandbar-built and include Pescadero 

Marsh, Drakes Bay, Drakes Estero, and Estero Americano (GFNMS 2010). Tomales Bay, Bodega 

Bay, and Bolinas Lagoon are moderately sized bays within the study region, while San Francisco 

Bay is located outside of the study region but has important influences on the region. Estuaries and 

bays are home to a range of ecosystems, including mudflats, brackish water, eelgrass beds, salt 

marshes, and tidal creeks (GFNMS 2010). Estuaries and bays are often highly productive because 

of warmer water temperatures, abundant light, and high nutrient levels. Many species of fish and 

invertebrates feed, spawn, and develop in estuaries and bays, including Pacific herring, smelt, 

sharks, rays, and Coho salmon, which is a federally threatened species (GFNMS 2008 and 2010). 

Pinnipeds use these habitats to haul out, breed, and feed, while dolphins forage, and birds like 

dowitchers, sandpipers, and ducks feed on burrowing organisms like clams, worms, crustaceans, 

and on plants and small fish (GFNMS 2010). 

Islands in the study region include the seven Farallon Islands, Año Nuevo Island, and other islands 

that are part of the Bureau of Land Management (BLM) California Coastal National Monument, 

Golden Gate National Recreation Area, and Point Reyes National Seashore. These islands are 

isolated, rocky habitats that allow marine animals to breed away from human activities. The waters 

surrounding these island habitats are highly productive, and they include a diverse and large 

assemblage of invertebrates, fishes, seabirds, and marine mammals (GFNMS 2010). For example, 

over 300,000 seabirds nest on the Farallon Islands annually from May-July (GFNMS 2008). Marine 

mammals including northern fur seals, elephant seals, harbor seals, California sea lions, and Steller 

sea lions breed on island habitats (GFNMS 2010).

Offshore habitats encompass a large portion of the study region and include a wide variety of 

ecosystems. Offshore pelagic ecosystems are located seaward of the 30m bottom contour, and they 

encompass the entire water column over the continental shelf and slope, from the surface to depths 

greater than 200m. As a result, offshore pelagic ecosystems can include surface waters and the deep 

sea. Shallow offshore pelagic ecosystems often contain newly-upwelled water, and can be 

influenced by the outflow of water from San Francisco Bay (GFNMS 2010). Offshore benthic 

ecosystems in the study region are found on the seafloor beyond shallow subtidal habitat, at depths 

ranging from 30-200m (Largier et al. 2010). Offshore pelagic habitat is extremely productive, with 

a diverse assemblage of organisms that includes phytoplankton, zooplankton, fishes, sea turtles, 

birds, and mammals. Two important species of krill, a critical food for many predators, are found in 

offshore pelagic ecosystems (GFNMS 2010 and references therein), as are fish including salmon, 

northern anchovy, rockfish, and one of the largest known concentrations of great white sharks in the 

world (GFNMS 2010). Cetaceans observed in offshore pelagic habitats include Pacific white-sided 

dolphin, Dall’s porpoise, and gray, humpback, and blue whales. 

Offshore deep-sea pelagic and benthic ecosystems (> 150m) are characterized by low light, cold 

water, and high pressure (GFNMS 2008 and 2010). Organisms found in offshore benthic zones 

include clams, mollusks, shrimp, crabs, sea urchins, deep-sea corals, and a variety of fishes on soft 

and hard bottoms (GFNMS 2008). 

20
Ocean Climate Indicators Monitoring Strategies: Physical

Physical Indicator #1: Air Temperature

BACKGROUND

Air temperature is a key indicator because it is a direct measure of climate change. Changes in air 

temperature indicate changes in weather and climate patterns, incoming radiation, the presence of 

marine layer clouds, and intertidal habitat suitability. Spatial patterns of variability in air 

temperature vary strongly, with some low-elevation coastal areas showing long-term cooling and 

other, more inland areas, experiencing warming. For example, mean annual air temperature at the 

South Farallon Islands showed an increasing trend from 1971 – 2012 (Figure 5) (Largier et al. 

2010). Climate change-induced variability in air temperature can be directly forced by the 

strengthened greenhouse effect or indirectly forced by other climate change impacts on the Northcentral California coast and ocean region, including strengthened upwelling and changing weather 

patterns. 

Figure 6. Annual maximum air temperature at Southeast Farallon Island from 1971 – 2012. The diagonal black 

line illustrates a linear regression indicating the trend in the data (Point Blue Conservation Science, unpublished 

data).

HABITATS OF INTEREST 

Air temperature is an important indicator in all habitats of the North-central California coast and 

ocean region, especially intertidal habitats. 

MEASUREMENT 

A technique for assessing regional-scale changes and trends in air temperature is via calibrated air 

temperature sensors in official weather stations used by the National Weather Service. Potential 

benchmarks include the length of a season and degree days (i.e., the number of days above or below 

a particular temperature standard). Specific techniques exist to assess smaller-scale regional or 

habitat-specific air temperature.

21
CASE STUDIES FOR MANAGEMENT 

Air temperature can be used by natural resource management in many ways, including the 

following:

• To identify when specific physiological responses associated with changes in air 

temperature are expected in intertidal and seabird species within the region, allowing 

management to determine if increased protection of these species is needed through the 

reduction of other disturbances. 

• To improve the design of seabird and other habitat restoration projects to allow for increased 

species resilience to potential future changes in air temperature. As an example, air 

temperature inside of Cassin’s auklet nests is being used by Point Blue Conservation 

Science on the Farallon Islands to better understand the response of Cassin’s auklets to heat 

stress and so that management can improve the design of restoration projects such as 

installing artificial nest boxes for these birds.

• To identify when action is needed to reduce non-climate stressors to increase resilience of 

elephant seals and other mammals in the region. As an example, ambient air temperature 

measurements are being compared with elephant seal body temperature by Sonoma State 

University and NPS. This information will increase understanding of the impacts of 

warming temperatures on elephant seals in the region, and may help to predict air 

temperatures above which elephant seal behavior changes.

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 2. Monitoring strategies and activities for air temperature

AIR TEMPERATURE MONITORING STRATEGY #1: 

Maintain existing monitoring of air temperature.

Need for Additional Funding & Infrastructure: 

$

Gaps in Research:

1. Continued evaluation of long-term temperature trends in the region is key to understanding 

change in the physical environment, and this requires ongoing observations.

2. There is a need for comparison between atmospheric and oceanic conditions, including 

interannual, decadal, and longer-timescale climate change.

3. What is the relationship between air temperature at land-based weather stations and in situ 

coastal and offshore air temperatures? 

4. Site-specific air temperature data is lacking, which is important for increased understanding 

of linkages with other indicators.

Activity 1.1: 

Encourage continued financial and technical support for monitoring of air temperature at weather 

stations throughout the North-central California coast, including at local scales.

Priority: 

Current and Potential Partners: 

• NWS

• National Data Buoy Center (NDBC)

• Central and Northern California Ocean Observing System (CeNCOOS)

• Bodega Marine Laboratory (BML)

• NPS weather stations

• Point Blue Conservation Science

Implementation Timeline:

22
Ongoing

AIR TEMPERATURE MONITORING STRATEGY #2:

Establish expanded local-scale monitoring in the North-central California coast and ocean region. 

Need for Additional Funding & Infrastructure: 

$

Gaps in Research:

1. Increased understanding of long-term changes in air temperature is needed in major habitats 

within the study region. 

Activity 2.1: 

Establish additional air temperature monitoring in critical habitats, especially in regions where 

changes can have a strong impact on biological indicators, as in intertidal and island habitats.

Priority: 

Current and Potential Partners:

• GFNMS, MBNMS, and CBNMS

• NPS

• California State Parks

• BML

• Romberg Tiburon Center (RTC)

• Point Blue Conservation Science

• Oikonos

• CeNCOOS

• Local and regional universities

• Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO)/ Multi Agency Rocky 

Intertidal Network (MARINe)

Implementation Timeline:

<1 year

EXISTING MONITORING 

Existing air temperature monitoring is detailed in the table below. Overall, existing monitoring is 

sufficient to assess large-scale temperature trends and changes. Support for additional and continued 

local air temperature monitoring is needed.

Table 3. Existing monitoring data sources for air temperature

AIR TEMPERATURE MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

Bodega Ocean 

Observing Node 

(BOON)

BML Shoreline 4/15/1988 –

3/31/2001

20-minute means, 

1 measurement/ 

second

BOON BML Shoreline 2/5/2001 –

1/1/2009

Every 10 seconds

BOON BML Shoreline 1/1/2009 –

present

Every 5 seconds

National Ocean 

Service (NOS) 

Center for 

Operational 

Oceanographic 

Point Reyes, CA 11/29/1999 –

present

Every 6 minutes

23
Products and 

Services (COOPS) Tidal 

Gauge Station# 

9415020

NDBC Buoy # 

46026

18 nautical miles 

West of San 

Francisco, near 

NDBC #46237

1982 – present Hourly http://www.ndbc.

noaa.gov/station_

history.php?statio

n=46026

NDBC Buoy 

#46013

Bodega Bay 1981 – present Hourly

NDBC Buoy 

#46012

Half Moon Bay, 

24 nautical miles 

South-Southwest 

of San Francisco

1980 – present Hourly

Point Blue 

Conservation 

Science Southeast 

Farallon Island 

Weather Station

Southeast 

Farallon Island

1971 – present Every 15 minutes Data is 

unpublished

AIR TEMPERATURE MONITORING - REANALYSIS DATA:

DATA SOURCE LOCATION OR

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

National Centers 

for 

Environmental 

Prediction 

(NCEP) Climate 

System Forecast 

Reanalysis v2 

(CSFR2)

Ranges 0.2° to 

2.5°.

1/1/2011 –

1/1/2013

Hourly, 6-hour, 

monthly

This is the same 

model used for 

the original CFSR 

Reanalysis, so if 

choose the same 

resolution, it is a 

seamless 

continuation. OR 

can choose higher 

resolution. 

http://rda.ucar.ed

u/datasets/ds094.

2/ 

NCEP North 

American 

Regional 

Reanalysis 

(NARR)

32km 1979 – present 3-hourly Most Organized 

Website at: 

http://rda.ucar.ed

u/datasets/ds608.

0/, also at: 

http://www.emc.n

cep.noaa.gov/mm

b/rreanl/#docs

24
Physical Indicator #2: Alongshore Wind Speed and Direction 

BACKGROUND 

Changes in alongshore wind speed and direction can indicate that there have been changes in

storminess in the region, or that there have been or will be changes in upwelling and associated 

nutrient availability along the North-central California coast. Wind speed is expected to strengthen 

as anthropogenic climate change continues, because climate change-induced warming occurs more 

quickly on land than in the ocean. This uneven heating is hypothesized to cause a greater land-sea 

heating contrast, leading to a larger land-sea pressure gradient and increased alongshore winds 

(Bakun 1990 and 2010). Analyses of alongshore winds in the study region support this hypothesis, 

with increased strength and duration of alongshore winds observed from the 1946 – 1990 (Schwing 

and Mendlessohn 1997; Mendelssohn and Schwing 2002), and between April and October from

1982 – 2007 (Garcia-Reyes and Largier 2010 and 2012; Largier et al. 2010). Wind observations can 

provide large-scale information about climate change impacts on the region, while high-resolution 

data provide information about the smaller-scale structure of wind patterns.

HABITATS OF INTEREST 

Alongshore wind speed and direction is a useful indicator in all habitats of the North-central 

California coast and ocean region, including in offshore habitats, where upwelling is a key oceanic 

process that affects nutrient delivery to surface waters, which in turn affects the availability of food 

for higher trophic levels.

MEASUREMENT 

A technique for measuring alongshore wind speed and direction in the study region is via calibrated 

wind speed and direction sensors in official weather stations used by the National Weather Service, 

in situ radar measurements, and remotely-sensed satellite and airplane observations. 

CASE STUDIES FOR MANAGEMENT 

Alongshore wind speed and direction can be used by natural resource management in many ways, 

including the following:

• To predict ocean productivity and food availability. As an example, wind data has been used 

by local researchers to evaluate upwelling along the North-central California coast, which 

has in turn been used by decision-makers and natural resource managers to predict 

productivity and the availability of food for higher trophic levels including salmon and other 

fish. These predictions can be used to guide fisheries management decisions.

• To evaluate the responses of seabirds to changes in the timing and strength of upwelling in 

the spring (the “spring transition”). 

• To improve public safety among sailors and kayakers who frequent the study region, which 

may be impacted by changes in the strength and predictability of wind speed and direction.

• To improve the selection of locations for restoration activities, the timing of restoration, and 

the restoration actions chosen. 

25
STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 4. Monitoring strategies and activities for wind speed and direction

WIND MONITORING STRATEGY #1: 

Maintain monitoring of alongshore wind speed and direction.

Need for Additional Funding & Infrastructure: 

$

Gaps in Research:

1. Existing in situ wind observations via offshore buoys have frequent time gaps, making it 

difficult to use these observations to verify remotely sensed offshore winds or to determine 

long-term trends in observed offshore winds.

2. Consistent wind observations are needed to allow for solid understanding of the long-term 

trend of wind speed and direction to help evaluate the impacts of climate change in the 

region

Activity 1.1: 

Maintain wind data collection at as high a 

quality as possible to minimize data gaps.

Activity 1.2: 

Repair/replace damaged wind sensors on 

offshore moorings and buoys with the goal of 

ensuring gaps in data of no longer than one 

month. Time could be reduced by collaboration 

between agencies by sharing vessels for repair.

Priority: Priority: 

Current and Potential Partners:

• NWS

• Local universities

• CeNCOOS

• NDBC

• NPS

Current and Potential Partners:

• NDBC

• GFNMS, CBNMS, and MBNMS

• Local universities

Implementation Timeline:

Ongoing

Implementation Timeline:

Ongoing

EXISTING MONITORING 

Existing monitoring of alongshore wind speed and direction is detailed in the table below. Overall, 

monitoring could be expanded to ensure high quality, reliable offshore in situ wind measurements, 

but this is not as high of a priority as expanding monitoring of other indicators. 

Table 5. Existing monitoring data sources for wind speed and direction

ALONGSHORE WIND SPEEED MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

BOON BML Shoreline 4/15/1988 –

3/31/2001

20-minute means, 

1 measurement/ 

second

Dataset called 

“Wind Speed and 

Direction

BOON BML Shoreline 5/1/2001 –

1/1/2009

Every 10 seconds Dataset called 

“Wind Speed and 

Direction

BOON BML Shoreline 1/1/2009 –

present

Every 1 second Dataset called 

“Wind Speed and 

Direction

26
BOON Cordell Bank 

Buoy

5/8/2007 –

6/15/2007, 

6/29/2007 –

8/21/2007, 

8/28/2007 –

3/30/2008

10-minute 

average collected 

once per hour

Dataset has 

“Average Wind 

Speed” and 

“Instantaneous 

Peak Wind 

Speed.” Data 

from 6/29/2007 –

8/21/2007 

sporadic.

NOS/CO-OPS 

Tidal Gauge 

Station# 9415020

Point Reyes, CA 10/1/1993 –

present

Every 6 minutes

NDBC Buoy 

#46012

Half Moon Bay, 

24 nautical miles 

South-Southwest 

of San Francisco

1980 – present Hourly Wind speed and 

wind direction 

data available

NDBC Buoy 

#46013

Bodega Bay 1981 – present Hourly Wind speed and 

wind direction 

data available

NDBC Buoy 

#46014

Point Arena 1981 – present Hourly http://www.ndbc.

noaa.gov/station_

page.php?station=

46014

NDBC Buoy # 

46026

18 nautical miles 

West of San 

Francisco, near 

NDBC #46237

1982 – present Hourly http://www.ndbc.

noaa.gov/station_

history.php?statio

n=46026

ALONGSHORE WIND SPEED MONITORING - SATELLITE DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

Oceansat-2 

Scatterometer 

(OSCAT) winds, 

12.5km

12.5km 9/2009 – present 12 hours http://manati.star.

nesdis.noaa.gov/d

atasets/OSCATD

ata.php?parname

=wv2

NASA Quick 

Scatterometer 

(QuickSCAT) 

winds, 12.5km

12.5km 1999 –

11/23/2009

Daily http://manati.star.

nesdis.noaa.gov/p

roducts/QuikSCA

T.php

ALONGSHORE WIND SPEED MONITORING - REANALYSIS DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

NCEP Climate 

System Forecast 

Reanalysis v2 

(CSFR2)

Ranges 0.2°-2.5°. Jan 1 2011 –

present (delay, 

actually available 

to July 2012)

Hourly, 6-hour, 

monthly

This is the same 

model used for 

the original CFSR 

Reanalysis, so if 

choose the same 

resolution, it is a 

27
seamless 

continuation. OR 

can choose higher 

resolution. 

http://rda.ucar.ed

u/datasets/ds094.

2/ 

Physical Indicator #3: Sea Surface Temperature 

BACKGROUND 

As with air temperature (Physical Indicator #1), sea surface temperature (SST) is a key parameter 

because it is a direct indicator of climate change and an indirect indicator of changes in upwelling, 

water transport, habitat suitability, and nutrients. Warming or cooling SST can, in turn, alter water 

column stratification and circulation, sea level (due to thermal expansion), and climate phenomena 

like hurricanes (Largier et al. 2010). While global average SST warmed by 0.1oC from 1961 – 2003 

(IPCC 2007), regional SST patterns are more complex both within and outside of the study region. 

Offshore and shore station temperatures have shown an increasing trend since 1955 (Largier et al.

2010 and references therein), but temperatures off of the central California coast, particularly near 

Bodega Head, decreased from 1982 – 2008. This observed cooling may reflect an increase in 

upwelling in the region, which may be due at least in part to anthropogenic climate change (Bakun 

et al. 1990 and 2010; Garcia-Reyes and Largier 2010; Largier et al. 2010). 

HABITATS OF INTEREST 

SST is a useful indicator in all habitats of the North-central California coast and ocean region 

because it has a direct impact on the biota in each habitat. It is particularly of interest in sandy 

beach, rocky shore, estuarine, and island habitats. 

MEASUREMENT 

A technique for measuring SST in the study region is via in situ thermistors, with accuracy to 0.1oC. 

High frequency measurements are preferred. It can also be measured via satellite or airplane.

CASE STUDIES FOR MANAGEMENT 

SST can be used by natural resource management in many ways, including the following:

• To predict changes in species range due to changes in the availability of habitat at a specific 

SST, and to evaluate the potential need to reduce high nutrient run-off and/or discharge. 

• To assess the risk for increasing harmful algal blooms, which can have important impacts on 

public safety for recreational visitors to beaches.

• To identify changes in upwelling strength, which can impact primary productivity and thus 

the productivity of the entire ecosystem. Such changes can be important to fisheries, and 

may result in managers considering catch limits to improve fish resilience. 

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 6. Monitoring strategies and activities for SST

SST MONITORING STRATEGY #1: 

Maintain existing local and regional-scale SST monitoring.

Need for Additional Funding & Infrastructure: 

$

Gaps in Research:

28
1. What are the spatial patterns of SST change?

2. How does temperature relate to other parameters, including chlorophyll?

Activity 1.1: 

Encourage continued financial and technical support for monitoring of local and regional SST in 

critical areas throughout the North-central California coast, including the Point Arena Mooring and 

such as estuaries Drakes Estero, Drakes Bay, and Estero Americano.

Priority: 

Current and Potential Partners:

• GFNMS, CBNMS, and MBNMS

• CeNCOOS

• NPS

• Local universities

• Point Blue Conservation Science

Implementation Timeline:

< 1 year

SST MONITORING STRATEGY #2: 

Ensure broad geographic and ecosystem coverage of SST monitoring.

Need for Additional Funding & Infrastructure: 

$$

Gaps in Research:

1. What are the spatial patterns of SST change?

2. How does SST relate to other parameters, including chlorophyll, air temperature, and wind 

speed?

Activity 2.1: 

Establish additional SST monitoring in critical areas, including estuarine, offshore, and intertidal 

habitats.

Priority: 

Current and Potential Partners:

• NPS

• California State Parks

• Oikonos

• CeNCOOS

• Local universities

Local community members

Implementation Timeline:

< 1 year

EXISTING MONITORING 

Existing SST monitoring is detailed in the table below. Overall, monitoring of SST is sufficiently 

broad. To ensure broad geographic coverage of all ecosystems in the region, there is a need for 

additional SST monitoring in Point Arena via mooring, in estuaries, and in offshore habitats.

29
Table 7. Existing monitoring data sources for SST

SST MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

BOON BML Shoreline 4/15/1988 –

8/31/2000

20-minute means, 

1 measurement/ 

second

Dataset for this 

and all BOON 

measurements 

below called 

“seawater 

temperature”

BOON BML Shoreline 9/1/2000 –

present

Every 10 seconds

BOON Fort Point 

Shoreline

7/10/2007 –

present

1 minute Dataset also 

available between 

10/8/2004 –

6/25/2007, but it 

is sporadic and 

has different 

sampling 

intervals

BOON BML Mooring 8/2004 –

1/4/2008 (old 

buoy) and 7/2010 

– present (new 

buoy)

5 minutes (old 

buoy) and 10 

minutes (new 

buoy)

BOON Cordell Bank 

Buoy

4/21/2009 –

1/26/2010, 

7/13/2010 –

8/19/2013

10-minute 

average collected 

once per hour

Dataset also 

available between 

5/8/2007–

9/10/2008, but it 

is sporadic and 

has different 

sampling 

intervals. Some 

data 

abnormalities 

present

BOON GFNMS 

Thermistor –

Bodega Head 

4/6/2009 –

present

Unspecified Dataset also 

available 

6/26/2005 –

3/24/2009, but 

sporadic

BOON GFNMS 

Thermistor –

Southeast 

Farallon Island

9/4/2008 –

present 

Unspecified Dataset also 

available 

6/26/2005 –

8/1/2008, but 

sporadic

BOON GFNMS 

Thermistor –

6/4/2007 –

11/7/2007 and 

Unspecified

30
Double Point 8/7/2008 –

12/4/2008

Bodega Line 

Oceanographic 

Transect

Offshore from 

BML and within 

Tomales Bay

2008 – present Monthly Available by 

request

Coastal Data 

Information 

Program (CDIP)

San Francisco 

Bay Buoy (#142) 

NDBC/WMO 

#46237

7/2007 – present 30 minutes

CDIP Cordell Bank 

Buoy (#029) 

NDBC/WMO 

#46214; 22 

nautical miles 

West of Point 

Reyes

12/1996 – 2/2004, 

4/2004 – 1/2009, 

9/2010 – present

30 minutes

NOS/CO-OPS 

Tidal Gauge 

Station# 9415020

Point Reyes 4/13/1992 –

present

Every 6 minutes Called “water

temperature”

Scripps Shore 

Station Program

Farallon Islands 1925 – 1943, and 

1977 – present

Daily Data from Aug 

2010 – Nov 2011 

may be off due to 

thermometer 

issues (+0.1 to -

0.6°C). Data 

collected by Point 

Blue 

Conservation 

Science.

CDIP San Francisco 

Buoy (#180) 

(farther in GF 

than #142); 

NDBC #46247

2/2011 – 11/2012 30 minutes Buoy 

decommissioned

NDBC Buoy 

#46012

Half Moon Bay, 

24 nautical miles 

South-Southwest 

of San Francisco

1980 – present Hourly

NDBC Buoy 

#46013

Bodega Bay 1981 – present Hourly

NDBC Buoy 

#46014

Point Arena 1981 – present Hourly http://www.ndbc.

noaa.gov/station_

page.php?station=

46014

NDBC Buoy # 

46026

18 nautical miles 

West of San 

Francisco, near 

NDBC #46237

1982 – present Hourly http://www.ndbc.

noaa.gov/station_

history.php?statio

n=46026

31
NDBC Buoy 

#46042

Monterey Bay 1987 – present Hourly http://www.ndbc.

noaa.gov/station_

page.php?station=

46042

SST MONITORING - SATELLITE DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

NOAA Polarorbiting 

Operational 

Environmental 

Satellites (POES) 

Advanced Very 

High Resolution 

Radiometer 

(AVHRR)

High Resolution 1985 – present Daily Data & plots 

available through 

Coastwatch: 

http://coastwatch.

pfel.noaa.gov/ind

ex.html

NOAA POES 

AVHRR 

Pathfinder V5.2

4km 1981– 2011 2x/day This is a 

reanalysis of 

AVHRR data, 

available at: 

http://www.nodc.

noaa.gov/Satellite

Data/pathfinder4k

m/ also at: 

http://www.nodc.

noaa.gov/sog/path

finder4km/ 

Group for HighResolution Sea 

Surface 

Temperature 

(GHRSST) 

climate data 

records

<10km Varies; higher 

resolution is more 

recent (ex 2008 –

present), lower 

resolution goes 

back to 1981

Varies http://www.nodc.

noaa.gov/Satellite

Data/ghrsst/

SST MONITORING - REANALYSIS DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

ERA-Interim ~0.7° 1979 – present 6-hourly or 

monthly mean

http://rda.ucar.ed

u/datasets/ds627.

2/ and 

http://www.ecmw

f.int/products/data

/archive/descripti

ons/ei/index.html. 

Background 

information about 

reanalysis 

products here: 

32
http://climatedata

guide.ucar.edu/re

analysis/erainterim 

NCEP CFSR Ranges 0.3° to 

2.5°, depending 

on grid selected 

and temporal 

frequency. 0.3° 

for diurnal 

monthly means; 

0.5° for regular 

monthly means

Jan 1 1979 – Jan 

1 2011

Hourly, diurnal 

monthly means, 

monthly means

http://rda.ucar.ed

u/datasets/ds093.

1/, 

http://rda.ucar.ed

u/datasets/ds093.

2, and 

http://rda.ucar.ed

u/pub/cfsr.html

CFSR2 Ranges 0.2° to 

2.5°.

Jan 1 2011 –

present (delay, 

actually to July 

2012)

Hourly, 6-hourly This is the same 

model used for 

the original CFSR 

Reanalysis, so if 

choose the same 

resolution, it is a 

seamless 

continuation. OR 

can choose higher 

resolution. 

http://rda.ucar.ed

u/datasets/ds094.

2/. Note that SST 

does not appear in 

the UCAR 

monthly CFSR 

page.

NCEP/National 

Center for 

Atmospheric 

Research 

(NCAR) Global 

Reanalysis 

Products

Ranges 1.8-2.5° 

(looks like SST is 

1.8° grid)

1948 – present 6-hourly or 

monthly mean

http://rda.ucar.ed

u/datasets/ds090.

0/

Physical Indicator #4: Sea Surface Salinity 

BACKGROUND 

Sea surface salinity (SSS) is primarily an indicator of changes in freshwater inputs, particularly in 

nearshore environments. Climate change can cause regional changes in SSS by altering water 

circulation and currents, vertical mixing, and freshwater input. 

HABITATS OF INTEREST 

SSS is a particularly useful indicator in nearshore habitats of the North-central California coast and 

ocean region, including sandy beach, rocky shore, estuarine, nearshore subtidal, and island habitats. 

33
MEASUREMENT 

A technique for measuring SSS in the study region is via conductivity measurements. Samples 

should be calibrated or checked using salinity analyses in a laboratory.

CASE STUDIES FOR MANAGEMENT 

SSS can be used by natural resource management in many ways, including the following:

• To track changes in the timing and magnitude of runoff, which can indicate changes in 

loading from the land that may alter the amount of biogenic material and contaminants in 

estuaries and bays. These changes can cause damage to farms, mariculture, and fisheries as 

during severe flooding in January 1982 and January 1998. GFNMS management can work

with upland resource managers to reduce nutrient loading during heavy storm events.

• To identify changes in ocean and coastal habitat zones, which can result in areas supporting 

a new and different biological community with less prey available for existing predators and 

more prey for new predators. Changes like this can affect species communities, especially 

fish. GFNMS and other managers can work to reduce non-climate stressors on fish 

communities.

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 8. Monitoring strategies and activities for SSS

SSS MONITORING STRATEGY #1: 

Expand monitoring of SSS in shoreline and offshore regions.

Need for Additional Funding & Infrastructure: 

$$

Gaps in Research:

1. To what extent does runoff or freshwater contribute to local biogeography?

2. Can salinity be related to other water quality constituents?

Activity 1.1: 

Establish a linear array of salinity monitoring 

sites along the North-central CA coast.

Activity 1.2: 

Add salinity monitoring to offshore NDBC buoy 

sites that are already measuring temperature.

Priority: Priority: 

Current and Potential Partners:

• GFNMS, CBNMS, and MBNMS

• Point Blue Conservation Science

• California Ocean Science Trust (OST)

• NPS

• Local universities

• Local government/agencies, including 

county water boards

• CA State Water Resources Control 

Board

Current and Potential Partners:

• NDBC

• CeNCOOS

• Local universities

Implementation Timeline:

< 1 year

Implementation Timeline:

< 1 year

EXISTING MONITORING 

Existing SSS monitoring is detailed in the table below. Overall, expanded monitoring of SSS is 

needed in nearshore sites, focused on the shoreline of the North-central California coast and ocean 

region. A linear array of monitoring sites is preferred. In areas where SSS monitoring is 

34
unavailable, local rainfall and stream discharge measurements can also be used to provide 

information about local changes in freshwater inputs, particularly in estuarine habitats.

Table 9. Existing monitoring data sources for SSS

SSS MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

BOON BML Shoreline 4/15/1988 –

4/2/1999

20-minute means, 

1 measurement/ 

second

BOON BML Shoreline 1/1/2001 –

present

Every 10 seconds

BOON Fort Point 

Shoreline

7/10/2007 –

present

1 minute Data also 

available between 

10/8/2004 –

6/25/2007, but it 

is sporadic and 

has different 

sampling 

intervals

BOON BML Mooring 8/2004 –

1/4/2008 (old 

buoy) and 7/2010 

– present (new 

buoy)

5 minutes (old 

buoy) and 10 

minutes (new 

buoy)

BOON Cordell Bank 

Buoy

4/21/2009 –

1/26/2010, 

7/13/2010 –

8/19/2013

10-minute 

average collected 

once per hour

Data also 

available between 

9/14/2007–

9/10/2008, but it 

is sporadic and 

has different 

sampling 

intervals and 

some data

abnormalities 

present before 

5/27/2008

Bodega Line 

Oceanographic 

Transect

Offshore from 

BML and within 

Tomales Bay

2008 – present Monthly Available by 

request

Scripps Shore 

Station Program

Farallon Islands 1925 – 1943, and 

1977 – present

Daily Data collected by 

Point Blue 

Conservation 

Science

NDBC Buoy # 

46026

18 nautical miles 

West of San 

Francisco, near 

NDBC #46237

1982 – present Hourly http://www.ndbc.

noaa.gov/station_

history.php?statio

n=46026

NDBC Buoy Bodega Bay 2007–2008 Hourly Data not 

35
#46013 consistently 

available 

throughout either 

year

Physical Indicator #5: Dissolved Oxygen 

BACKGROUND 

Dissolved oxygen (DO) is a key biologically-influenced water property that can indicate changes in 

habitat suitability, water quality, primary productivity, and degradation of organic matter. Because 

all macroscopic organisms require oxygen, changes in DO can have cascading impacts on the entire 

ecosystem. Typically, surface waters contain higher levels of DO than subsurface waters due to 

photosynthesis and diffusion from the oxygen-rich atmosphere. These oxygen-enriched waters are 

transported throughout the water column by ocean currents and vertical mixing. Climate change can 

cause regional changes in DO by altering water circulation and currents, vertical mixing, air-sea 

oxygen exchange, and biological production and respiration; these impacts can co-occur with ocean 

acidification, discussed below (Largier et al. 2010 and references therein).

HABITATS OF INTEREST 

DO is a particularly useful indicator in nearshore subtidal, and offshore habitats, where it is affected 

by changes in air-sea oxygen exchange, circulation, and organism respiration. It is also important in 

estuarine habitats, where changes in DO are indicative of changes in eutrophication. Benthic

organisms that cannot easily move are particularly vulnerable to shifts from high to low DO.

MEASUREMENT 

A technique for measuring DO in the study region is via in situ electronic or optical sensors, with 

accuracy to 0.1 mL/L. Calibration should be developed with titration in a lab. 

CASE STUDIES FOR MANAGEMENT 

DO can be used by natural resource management in many ways, including the following:

• To evaluate shoaling or expansion of oxygen minimum zones (OMZs) (Bograd et al. 2008; 

Koslow et al. 2011), as is being done off the Oregon coast (Grantham et al. 2004), and 

which can have important impacts on fish and invertebrates (Keller et al. 2010; Koslow et al. 

2011). Migration of OMZs into shallower continental shelf waters would be a major threat 

to species in areas adjacent to the shelf break. Natural resource managers can adjust fishing 

limits to help reduce the impact on affected species.

• To establish integration with monitoring of ocean chemistry, which can allow for improved 

understanding of habitat suitability in the region. 

• To evaluate local-scale ocean acidification remediation or mitigation tactics and their 

efficacy, such as the restoration of seagrass beds for carbon sequestration.

• To facilitate the identification of biogenic habitats that are at the highest risk from 

acidification. GFNMS managers can develop additional protections for these habitats that 

can help to reduce or eliminate other anthropogenic impacts. 

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 10. Monitoring strategies and activities for DO

DO MONITORING STRATEGY #1: 

Expand monitoring of DO along the North-central California coast.

Need for Additional Funding & Infrastructure: 

36
Activity 1.1: $-$$

Activity 1.2: $$$ 

Gaps in Research:

1. Are we observing changes in the OMZ?

2. What are the relationships between changing pH and changing DO, which may co-occur 

within the study region? 

3. Are offshore changes correlated with conditions in San Francisco Bay? Is this linked to the 

growing concern about hypoxic waters in San Francisco Bay? 

Activity 1.1: 

Add oxygen sensors to existing moorings and 

surveys, especially in nearshore subtidal and 

estuarine habitats.

Activity 1.2: 

Add new moorings that measure DO in 

nearshore subtidal, estuarine, and offshore

habitats.

Priority: Priority: 

Current and Potential Partners:

• GFNMS, CBNMS, and MBNMS

• Applied California Current Ecosystem 

Studies (ACCESS)

• Point Blue Conservation Science

• Local universities

• Commercial fisheries

• West Coast Ocean Acidification and 

Hypoxia Science Panel

• West Coast Governors Alliance on 

Ocean Health

Current and Potential Partners:

• GFNMS, CBNMS, and MBNMS

• ACCESS

• Point Blue Conservation Science

• Local universities

• Commercial fisheries

• West Coast Ocean Acidification and 

Hypoxia Science Panel

• West Coast Governors Alliance on 

Ocean Health

Implementation Timeline:

~ 1 year

Implementation Timeline:

~ 1 year

EXISTING MONITORING 

Existing DO monitoring is detailed in the table below. Overall, existing monitoring of DO is not 

sufficient to address the Indicators Monitoring Objectives. Expanded monitoring of DO is needed in 

existing surveys and moorings, including calibration and regular sample analysis. New moorings 

are also needed to ensure sufficient DO monitoring. 

Table 11. Existing monitoring data sources for DO

DISSOLVED OXYGEN MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

ACCESS Cruise 

Data

Cruise lines 2004 – present 3-4 times 

annually, AprilOctober

Partnership 

between Point 

Blue 

Conservation 

Science and 

GFNMS

BOON BML Mooring July 2010 –

present

Every 10 minutes http://bml.ucdavis

.edu/boon/bml_bu

oy.html

Bodega Line 

Oceanographic 

Offshore from 

BML and within 

2008 – present Monthly Available by 

request

37
Transect Tomales Bay

Bodega Ocean 

Acidification 

Research 

(BOAR) 

Tomales Bay August 2012 –

present

Every 30 minutes Available by 

request. 

http://bml.ucdavis

.edu/research/rese

archprograms/climate

-

change/oceanacid

ification/

Physical Indicator #6: Ocean Chemistry

BACKGROUND 

As with air temperature and SST, ocean acidification (OA) is a direct impact of increasing carbon 

dioxide (CO2) emissions into the atmosphere and subsequent diffusion through the atmosphereocean interface. As humans continue to emit increasing amounts of CO2 into the atmosphere, a 

significant portion of these emissions are absorbed by the Earth’s oceans. When CO2 is dissolved 

into seawater, a chemical reaction causes increased ocean acidity and reduced carbonate 

availability; this can impact marine organisms in a myriad of different ways, including shell 

calcification, respiration, and reproduction (Kleypas et al. 1999; Caldeira and Wickett 2003). 

Changes in ocean chemistry have been documented to have significant impacts on organisms 

studied in the laboratory and field, including local examples such as foraminifera, pteropods, 

mussels, oysters, and crabs (e.g. Doney et al. 2009; Largier et al. 2010 and references therein). 

As a result, ocean chemistry (including, pH, carbonate saturation state) is a key indicator of OA and 

associated impacts on marine organisms (Kleypas et al. 1999; Caldeira and Wickett 2003). Ocean 

acidification is already causing documented shifts in pH and saturation state within the California 

Current (Feely et al. 2008), and these shifts are predicted to exacerbate in the future (Hauri et al. 

2009).

HABITATS OF INTEREST 

Measures of ocean chemistry such as carbonate saturation state are particularly useful indicators in 

rocky intertidal, nearshore subtidal, estuarine, and offshore habitats. 

MEASUREMENT 

Efforts are underway to develop an understanding of the regional relationships between ocean 

chemistry (pH) and other parameters (temperature, salinity, dissolved oxygen); a knowledge of 

these relationships will allow for the development of algorithms to calculate saturation state in the 

absence of discrete bottle sampling, described below (e.g., Juranek et al. 2009).

There are four frequently used measures of ocean chemistry, all of which rely on analysis of in situ 

water samples (i.e., “discrete bottle sampling”). Ideally, two of the four should always be measured:

1. Dissolved inorganic carbon (DIC): Should be measured with spectroscopy or infrared 

analysis of water samples. 

2. pH: Best to use spectrophotometric or durafet measurements. It is not preferable to use glass 

electrodes unless they are carefully calibrated and strongly supported by discrete bottle 

sampling.

3. Total alkalinity: Measured via titration.

38
4. pCO2: Best measured via coulometric analysis of water samples.

CASE STUDIES FOR MANAGEMENT 

Ocean chemistry monitoring data can be used by natural resource management in many ways, 

including the following:

• To evaluate and predict the impact of changes in ocean chemistry, including OA, on 

local/regional productivity and ecosystems. For example, reproductive failure in 

recreationally valuable mussel species and other bivalves can impact sustainable 

aquaculture, with important economic and ecological effects on the region.

• To evaluate local-scale ocean acidification remediation or mitigation tactics and their 

efficacy, such as the restoration of seagrass beds for carbon sequestration. 

• As with DO, to facilitate the identification of biogenic habitats that are of the highest risk 

from acidification. GFNMS managers can develop additional protections for these habitats 

that can help to reduce or eliminate other anthropogenic impacts. 

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 12. Monitoring strategies and activities for ocean chemistry

OCEAN CHEMISTRY MONITORING STRATEGY #1: 

Expand the geographic coverage of ocean chemistry monitoring.

Need for Additional Funding & Infrastructure: 

$$

Gaps in Research:

1. Do organisms respond to average carbonate chemistry conditions, and/or changes in the 

variability (seasonal, monthly, daily) of these parameters? 

2. What is the impact of combined influence of low-pH and low oxygen waters, which may cooccur within the study region? 

3. How does ocean chemistry influence local productivity and food webs, and vice versa? 

Activity 1.1:

Add pH and pCO2 instruments to existing 

moorings and offshore cruises; support with 

discrete bottle samples.

Activity 1.2:

Expand monitoring of ocean chemistry in 

critical habitats, including moorings and 

surveys.

Priority: Priority: 

Current and Potential Partners:

• GFNMS

• CeNCOOS

• California State Water Board

• Regional water boards 

• Local universities

• Ocean Margin Ecosystems Group for 

Acidification Studies (OMEGAS) 

partner universities

• PISCO/MARINe

• Pacific Marine Environmental 

Laboratory (PMEL)

• West Coast Ocean Acidification and 

Hypoxia Science Panel 

• West Coast Governors Alliance on 

Current and Potential Partners:

• GFNMS

• CeNCOOS

• California State Water Board

• Regional water boards

• Local universities, including UC Davis 

and the OMEGAS program

• PISCO/MARINe

• PMEL

• West Coast Ocean Acidification and 

Hypoxia Science Panel

• West Coast Governors Alliance on 

Ocean Health

39
Ocean Health

Implementation Timeline:

<1 year 

Implementation Timeline:

~ 1-2 years 

EXISTING MONITORING 

Existing ocean chemistry monitoring is detailed in the table below. Overall, existing monitoring of 

ocean chemistry is not sufficient to address the Indicators Monitoring Objectives. The geographic 

coverage of ocean chemistry monitoring could be expanded, with a focus on nearshore 

communities. 

Table 13. Existing monitoring data sources for ocean chemistry

Physical Indicator #7: Wave Height and Direction 

BACKGROUND 

Wave height and direction indicate changes in inundation time, storminess, shoreline erosion, beach 

condition, opening and closing of estuary mouths, agitation of coastal bottom and shoreline biota, 

and habitat suitability in the North-central California coast and ocean region. It is a key indicator 

because the stability of shoreline communities in the region depends on wave height and direction. 

Climate change can modify wave height and direction due to altered atmospheric circulation and 

sea surface temperature.

HABITATS OF INTEREST 

Wave height and direction are particularly useful indicators in shoreline habitats of the Northcentral California coast and ocean region, especially nearshore subtidal, rocky shore, sandy beach, 

island, and estuarine habitats. 

OCEAN CHEMISTRY MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

Bodega Line 

Oceanographic 

Transect

Offshore from 

BML and within 

Tomales Bay

2008 – present Monthly Available by 

request

BOAR Sensors located 

offshore Bodega 

Head, in Tomales 

Bay, and along 

shoreline in 

northern 

California; 

monitoring of 

individual shorebased sites (bottle 

samples)

2011 – current 30-60min Available by 

request. More 

information at: 

http://bml.ucdavis

.edu/research/rese

archprograms/cli

matechange/ocea

nacidification/

ACCESS Cruise 

Data

ACCESS lines 2013 – present 3-4 times 

annually, AprilOctober

Partnership 

between Point 

Blue 

Conservation 

Science and 

GFNMS

40
MEASUREMENT 

A technique for measuring wave height and direction in the study region is via buoys. 

CASE STUDIES FOR MANAGEMENT 

Wave height and direction can be used by natural resource management in many ways, including 

the following:

• To evaluate the impacts of changes in storminess on the study region. As an example, Our 

Coast – Our Future (OCOF) provides online decision support tools that allow for visualization 

of the impacts of sea level rise and storms, including wave heights, along the North-central 

California coast. Managers can use OCOF to evaluate the potential impacts of flooding and 

changes in wave height, and to adjust restoration, construction, or management plans as a 

result.

• To predict the timing of closure of the mouth of Estero Americano, Estero de San Antonio, 

and the mouth of the Russian River, and other bar-built estuaries. GFNMS management can 

identify if there is a need to work with state and federal agencies on the maintenance of barclosures and the necessity of manually opening or closing these estuaries.

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 14. Monitoring strategies and activities for wave height and direction

WAVE HEIGHT & DIRECTION MONITORING STRATEGY #1: 

Maintain existing monitoring of wave height and direction with buoys.

Need for Additional Funding & Infrastructure: 

$$

Gaps in Research:

Long-term wave data are needed to understand climate-scale changes in wave height direction

Activity 1.1: 

Encourage continued financial and technical support for existing monitoring of wave height and 

direction, including on buoys.

Priority: 

Current and Potential Partners:

NDBC

CeNCOOS, Pacific Coast Ocean Observing System (PaCOOS), and United States Integrated Ocean 

Observing System (IOOS)

Point Blue Conservation Science

Local universities

Local research laboratories including BML and RTC

NPS

USGS

Implementation Timeline:

Ongoing

WAVE HEIGHT & DIRECTION MONITORING STRATEGY #2: 

Establish expanded monitoring of wave height and direction with buoys.

Need for Additional Funding & Infrastructure: 

$$$

Gaps in Research:

Small spatial scale changes in wave height and direction can have important impacts on estuaries 

and other coastal locations and therefore need to be better understood.

41
Activity 2.1: 

Establish new monitoring of wave height and direction in critical locations, including offshore, 

nearshore, and the mouths of estuarine habitats.

Priority: 

Current and Potential Partners:

NDBC

CeNCOOS, PaCOOS, and IOOS

Point Blue Conservation Science

Local universities

Local research laboratories including BML and RTC

NPS

USGS

Implementation Timeline:

<1 year

WAVE HEIGHT & DIRECTION MONITORING STRATEGY #3: 

Utilize monitoring of wave height to allow for high-resolution wave datasets.

Need for Additional Funding & Infrastructure: 

$$

Gaps in Research:

Extremely high-resolution wave observations are not currently available. Because wave models are 

more deterministic than other models, they are very useful tools and can provide a good dataset for 

use by management.

Activity 3.1: 

Support modeling of wave height and direction, which is more deterministic than other ocean 

modeling products.

Priority: 

Current and Potential Partners:

Local universities

USGS

Implementation Timeline:

~1 year

EXISTING MONITORING 

Existing monitoring of wave height and direction is detailed in the table below.

Table 15. Existing monitoring data sources for wave height and direction

WAVE HEIGHT AND DIRECTION MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

CDIP San Francisco 

Buoy (#142); 

NDBC/WMO 

#46237

7/26/2007 –

present

30 minutes 9-band Wave 

Energy and 

Direction, 

converted to 

available daily 

maximum wave 

height as well

42
CDIP San Francisco 

Buoy (#180); 

NDBC/WMO 

#46247

2/2011 – 11/2012 30 minutes Buoy 

decommissioned; 

9-band Wave 

Energy and 

Direction, 

converted to 

available daily 

maximum wave 

height as well

NDBC Buoy 

#46013

Bodega Bay 1981 – present Hourly “Significant wave 

height”, swell 

direction, and 

wind-wave 

direction 

available

NDBC Buoy 

#46012

Half Moon Bay, 

24 nautical miles 

South-Southwest 

of San Francisco

1980 – present Hourly “Significant wave 

height”, swell 

direction, and 

wind-wave 

direction 

available

Physical Indicator #8: Sea Level 

BACKGROUND 

Sea level is a key indicator of climate change in the North-central California coast and ocean region 

because it is a direct response of the ocean to climate change. As the global average ocean 

temperature has continued to warm, thermal expansion and the melting of land-based glaciers have 

caused sea level to increase. Long-term sea level trends are consistent in the region, showing a sea 

level rise of approximately 2mm/year (e.g., Bromirski et al. 2011). 

In recent decades, however, sea level has actually decreased along the North-central California 

coast (e.g., Bromirski et al. 2011). It has been hypothesized that the current cold phase of the Pacific 

Decadal Oscillation is a major cause of the recent sea level decrease (Bromirski et al. 2011; Parris et 

al. 2012 and references therein), although this is not settled in the literature. Other confounding 

factors for sea level include tectonic movements, tides, and non-anthropogenic changes in local 

wind and waves.

HABITATS OF INTEREST 

Sea level is especially important in nearshore subtidal, rocky shore, and estuarine habitats. 

MEASUREMENT 

A technique for measuring sea level in the study region is via official in situ tide gauge 

observations, many of which are provided by NOAA National Ocean Service (NOS) Center for 

Operational Oceanographic Products and Services (CO-OPS), and by USGS. 

CASE STUDIES FOR MANAGEMENT 

Sea level change data can be used by natural resource management in many ways, including the 

following:

43
In the context of long-term coastal planning:

• To determine if vulnerable habitat is currently protected.

• To determine if there are areas protected by seawalls that prevent marine species from moving 

shoreward. If so, are there ways to restore habitat or otherwise reduce species vulnerability in 

these areas?

• To plan for wetland restoration projects. As an example, in the Giacomini Wetland 

Restoration Project, wetland restoration was modified to accommodate sea level rise and 

associated changes in biogenic habitat. 

• To evaluate the potential impacts of sea level changes in the region. As described for Physical 

Indicator #7 – Wave Height, Our Coast–Our Future provides sea level rise decision support 

tools for the study region. It uses a newly developed high resolution digital elevation model 

and best available sea level rise projections, and has already been used by managers to 

determine the best location to relocate park facilities that faced inundation due to sea level 

rise.

• To identify locations where seabird, shorebird, and pinniped habitats are threatened, and to 

work to reduce non-climate stressors to increase their resilience. This is because sea level rise 

can greatly impact seabirds, shorebirds, and pinnipeds that live in coastal habitats. Increasing 

sea level reduces the habitat available for birds and pinnipeds, and can result in mortality of 

these animals. 

• To inform decisions about the need for potential re-surveying of GFNMS boundaries. The 

shoreline boundary of GFNMS and MBNMS is the mean-high-water line mark. As sea level 

changes, so can the landward boundary of GFNMS.

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 16. Monitoring strategies and activities for sea level

SEA LEVEL MONITORING STRATEGY #1: 

Ensure that existing sea level monitoring is maintained at tide gauges along the North-central 

California coastline and in San Francisco Bay.

Need for Additional Funding & Infrastructure: 

$

Gaps in Research:

An increased understanding of the interaction between sea level rise and erosion/sediment transport 

is needed.

Activity 1.1:

Support sustained financial resources for valuable long-term tide gauge sea level monitoring, which 

is vital for supporting comparisons within the region and between partners.

Priority: 

Current and Potential Partners:

CO-OPS

USGS

Local universities

BML

Point Blue Conservation Science

NPS

Other sea level data-users

Implementation Timeline:

Ongoing

44
SEA LEVEL MONITORING STRATEGY #2:

Establish new monitoring of sea level at local scales.

Need for Additional Funding & Infrastructure: 

$$-$$$

Gaps in Research:

In addition to changes in the long-term trends of sea level, variability is also changing, and it is best 

identified at local scales.

Activity 2.1:

Establish new sea level monitoring at more closely spaced sites, particularly in critical habitats, to 

enhance the ability to identify local scale changes in sea level. 

Priority: 

Current and Potential Partners:

GFNMS

OCOF

BML

Point Blue Conservation Science

California Coastal Commission

California Ocean Protection Council

Other federal agencies

Implementation Timeline:

<1 year

EXISTING MONITORING 

Existing monitoring of sea level is detailed in the table below. Overall, monitoring of sea level is 

sufficient in the North-central California coast. Existing tide gauges show a consistent pattern along 

the study region, and along most of the California coast.

Table 17. Existing monitoring data sources for sea level

SEA LEVEL MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

NOS/CO-OPS 

Tidal Gauge 

Station# 9414290

San Francisco, 

CA

6/30//1854 –

present

Every 6 minutes, 

hourly, or 

monthly

Verified hourly 

data available 

since 6/30/1854

NOS/CO-OPS 

Tidal Gauge 

Station# 9415020

Point Reyes, CA 1/1/1975 –

present

Every 6 minutes, 

hourly, or 

monthly

Verified hourly 

data since 

1/1/1975; hourly 

and 6-min data 

since 1/1/1996

45
Ocean Climate Indicators Monitoring Strategies: Biological

Biological Indicator #1: Primary Productivity

BACKGROUND 

Primary productivity is a vitally important indicator that serves as the foundation of the ecosystem 

indicators contained in this report. Primary producers in the region include phytoplankton, algae, 

seagrass, and kelp. Changes in primary productivity, as measured by changes in primary producer 

biomass, can indicate changes in the lowest trophic levels of the food web, the potential for harmful 

algal blooms, and the success of management actions to mitigate the impacts of climate change on 

the coast and ocean region. 

Please note that an expanded discussion of large habitat-forming primary producers such as kelp 

and seagrass can be found in Biological Indicator #3: Spatial extent of habitat-forming organisms. 

HABITATS OF INTEREST 

Primary producer biomass is a particularly useful indicator in all habitats because it is the 

foundation of the aquatic food web.

MEASUREMENT 

A proxy for measuring primary producer biomass (as chlorophyll-a) in pelagic areas of the study 

region is via analysis of water samples with a fluorometer or by extraction of chlorophyll. It can 

also be measured via sensors on satellites or airplanes, as with the Moderate Resolution Imaging 

Spectroradiometer (MODIS). Benthic primary producer biomass in rocky intertidal areas can be 

assessed directly by sampling in benthic quadrats. 

CASE STUDIES FOR MANAGEMENT 

Primary Productivity can be used by natural resource management in many ways, including the 

following:

• To determine food availability in pelagic ecosystems and habitat availability in benthic 

ecosystems. A reduction in either would provide a warning that other stressors need to be 

reduced to protect fish and other species.

• To help predict the overall health of the ecosystem and abundance of mid and upper trophic 

groups. It is often the first biological response to physical changes. It is important to note 

that very high levels of primary productivity can result in phytoplankton blooms causing low 

oxygen conditions, thus negatively impacting the overall health of an ecosystem. 

• To provide a warning of harmful algal blooms through data on phytoplankton species 

composition.

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 18. Monitoring strategies and activities for primary productivity

PRIMARY PRODUCTIVITY MONITORING STRATEGY #1: 

Maintain existing monitoring of chlorophyll and ensure that measurements are calibrated.

Need for Additional Funding & Infrastructure: 

$-$$

Gaps in Research: 

1. Long-term observations of primary productivity are needed to ensure ability to identify 

climate-related changes.

2. A better understanding of the causes of an observed disconnect between reduced primary 

46
productivity and fish populations in the study regions since 2007 is needed.

Activity 1.1:

Support continued funding for existing 

chlorophyll monitoring.

Activity 1.2:

Check chlorophyll seawater samples for 

calibration.

Priority: Priority: 

Current and Potential Partners:

• Local universities

• Point Blue Conservation Science

• NOAA

Current and Potential Partners:

• Local universities

• Point Blue Conservation Science

Implementation Timeline:

Ongoing

Implementation Timeline:

~ 1 year

PRIMARY PRODUCTIVITY STRATEGY #2: 

Expand measurement of primary productivity via sensors on moorings and surveys, being careful to 

maintain good quality control.

Need for Additional Funding & Infrastructure: 

$$

Gaps in Research:

1. Lack of existing in-situ monitoring on a regular basis

2. Increased nutrient sampling is needed to allow for improved primary productivity 

projections and increased knowledge about eutrophication in estuarine habitats.

Activity 2.1:

Expand chlorophyll monitoring at shoreline 

stations and at existing moorings and surveys.

Activity 2.2:

Add nutrient sampling to existing moorings and 

surveys.

Priority: Priority: 

Current and Potential Partners:

• Local universities

• Point Blue Conservation Science

• NDBC

Current and Potential Partners:

• Local universities

• Point Blue Conservation Science

• NPS

Implementation Timeline:

~ 1 year

Implementation Timeline:

~ 1 year

PRIMARY PRODUCTIVITY MONITORING STRATEGY #3:

Establish harmful algal bloom monitoring by quantifying phytoplankton assemblages.

Need for Additional Funding & Infrastructure:

$$

Gaps in Research:

1. Increased monitoring of harmful algal blooms is needed.

2. Increased ability to predict harmful algal blooms is needed.

Activity 2.1:

Sample phytoplankton assemblages periodically at set observing stations alongshore, with more 

intensive monitoring during harmful algal bloom events.

Priority: 

Current and Potential Partners:

• GFNMS, CBNMS, and MBNMS

• NOAA

47
• CA Department of Public Health

• Point Blue Conservation Science

• Local universities

Implementation Timeline:

~ 1 year

PRIMARY PRODUCTIVITY MONITORING STRATEGY #4: 

Increase availability of remote monitoring of primary producer biomass.

Need for Additional Funding & Infrastructure: 

$$-$$$, depending on the technology being used, and if that technology is already in use in a 

region.

Gaps in Research:

1. Need to have the ability to compare surface imagery and biomass, as with multispectral kelp 

canopy surveys and rocky intertidal algae.

Activity 3.1:

Use hyperspectral imaging to monitor seagrass, kelp, and large algal blooms, ensuring that 

measurements are ground-truthed.

Priority: 

Current and Potential Partners:

• NOAA

• CDFW

Implementation Timeline:

~ 1 year

EXISTING MONITORING 

Existing primary productivity monitoring is detailed in the table below. Overall, primary producer 

biomass is not measured routinely except some phytoplankton analysis by the California 

Department of Public Health, and sporadic measurements of algal cover in the intertidal. Note that 

the California Cooperative Oceanic Fisheries Investigations (CalCOFI) is a valuable source of 

primary productivity and monitoring data for many physical indicators, but because data collection 

is focused on the region from San Diego to Point Conception, it is not listed in this data sources 

table. Overall, monitoring of primary productivity needs to be expanded and integrated. 

Table 19. Existing monitoring data sources for primary productivity

PRIMARY PRODUCTIVITY MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

PISCO/MARINe Numerous sites 

along CA coast

Unspecified Unspecified http://data.piscow

eb.org/DataCatalo

gAccess/DataCat

alogAccess.html

ACCESS Cruises Cruise lines May 2004 –

present 

3-4 cruises from 

April – October 

annually

Partnership 

between Point 

Blue 

Conservation 

Science and 

GFNMS; 

Phytoplankton 

48
abundance 

collected to 

supplement 

California 

Department of 

Public Health 

monitoring, 

below.

California 

Department of 

Public Health

Numerous 

stations along CA 

coast 

1993 – present Monthly Volunteer-based 

monitoring of 

toxic 

phytoplankton; 

http://www.cdph.

ca.gov/HealthInfo

/environhealth/wa

ter/Pages/phytopl

anktonmonitoring

program.aspx

PRIMARY PRODUCTIVITY MONITORING - SATELLITE DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

MODIS through

Coastwatch

Ranges, high 

resolution

Unspecified Daily http://coastwatch.

noaa.gov/cwn/cw

_products_oc.htm

l

Visible Infrared 

Imaging 

Radiometer Suite 

(VIIRS) through 

Coastwatch

4km Unspecified Unspecified http://coastwatch.

noaa.gov/cwn/cw

_products_oc.htm

l

Biological Indicator #2: Mid-Trophic Level Species Abundance, Biomass, & Phenology 

BACKGROUND 

Changes in mid-trophic level species abundance, biomass, 

and phenology can indicate changes in the health of the 

middle trophic levels of the food web. This indicator is 

intentionally broad because it provides the flexibility 

needed to choose the best possible selected species for 

each habitat within the study region. 

The Indicators Working Group identified selected species 

for major habitat types within the study region, and these 

are provided in Table 20 below. In identifying these 

selected species, working group members focused on 

native species and avoided selecting fished species except 

when they were key to an ecosystem’s health. Note that 

these selected species were identified based on currently available monitoring data, and they 

Figure 7. Giant Green Anemone

49
represent a shortlist among many possible mid-trophic level species in the North-central California 

coast and ocean region. The abundance of rocky intertidal selected species is a reflection of the 

relatively long history of monitoring in this habitat. Some species, which would provide valuable 

information if long-term datasets were underway or already available, have been designated as 

promising species and are provided in Appendix F.

Table 20. Selected mid-trophic level species by habitat type

SELECTED MID-TROPHIC LEVEL SPECIES

SANDY BEACH

Mole crab (Emerita analoga)

ROCKY INTERTIDAL

California mussel (Mytilus californianus)

Ochre sea star (Pisaster ochraceus) 

Gooseneck barnacle (Pollicipes polymerus)

Giant green (Anthopleura xanthogrammica) & 

Sunburst anemone (Anthopleura sola)

Volcano barnacle (Tetraclita rubescens)

ESTUARIES & BAYS

Gaper clam (Tresus capax and/or Tresus nuttalli)

Staghorn sculpin (Leptocottus armatus)

Shiner surfperch (Cymatogaster aggregata)

NEARSHORE SUBTIDAL

Blue (Sebastes mystinus) and Gopher (Sebastes 

carnatus) rockfish

Cabezon (Scorpaenichthys marmoratus)

OFFSHORE (BENTHIC & PELAGIC)

Copepods (e.g., Pseudocalanus mimus in boreal 

and Calanus pacificus in transition zone) 

Shortbelly rockfish (Sebastes jordani)

Pteropods (e.g., Clione limacina and Limacina 

helicina)

HABITATS OF INTEREST 

Mid-trophic level species abundance, biomass, and phenology are particularly useful indicators in 

all habitat types in the North-central California coast and ocean region. 

MEASUREMENT 

Techniques for measuring mid-trophic level species abundance, biomass, and phenology in the 

study region vary by organism and habitat type. 

CASE STUDIES FOR MANAGEMENT 

Abundance, biomass, and phenology of mid-trophic level species can be used by natural resource 

management in many ways, including the following:

• To identify vulnerable populations of mid-trophic species, and to reduce non-climate 

stressors on these species to increase their resilience to climate change.

• To provide an ‘early warning system’ about ocean chemistry, including OA, in a region. 

• To identify the impacts of climate change on California mussels, which are a foundation 

species in the study region. Because mussel beds support hundreds of other species within 

50
the mussel matrix, decreases in California mussel populations could have large impacts on 

many other species, including some higher tropic level organisms and economic impacts on 

the region. Evaluations of the connections between California mussels and wave action are 

already being done on Southeast Farallon Island and could be applied anywhere in the study 

region.

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 21. Monitoring strategies and activities for mid-trophic species

MID-TROPHIC SPECIES MONITORING STRATEGY #1: 

Maintain monitoring of mid-trophic level selected species.

Need for Additional Funding & Infrastructure: 

$$$

Gaps in Research:

1. A common output format with metadata for datasets from multiple monitoring programs is 

needed, because this gap in data management might hinder synthetic research.

2. Ensuring long-term data collection is needed so that climate-scale changes in mid-trophic 

species can be identified.

Activity 1.1:

Maintain current monitoring of mid-trophic selected species. 

Priority:

Current and Potential Partners:

• GFNMS

• PISCO/MARINe

• Monterey Bay Aquarium Research Institute (MBARI)

• BML

• ACCESS

• Point Blue Conservation Science

• Farallon Institute

• CDFW

• California Ocean Protection Council

• NMFS

• NPS

• California Academy of Sciences

• OST

• Local universities, including Sonoma State University, San Francisco State University, and 

UC Davis

Implementation Timeline:

Ongoing

MID-TROPHIC SPECIES MONITORING STRATEGY #2:

Expand monitoring of mid-trophic level selected species and increase frequency of existing 

monitoring. 

Need for Additional Funding & Infrastructure: 

$$$

Gaps in Research:

1. Spatial and temporal gaps in monitoring need to be filled by adding new sites and 

monitoring more frequently, especially those that are located away from anthropogenic 

factors. This will help to identify connections between key habitats, including South 

51
Farallon Island, Duxbury Reef, Fitzgerald Marine Reserve, and PISCO/MARINe/National 

Park Service monitored sites. Supporting and investing in citizen science and volunteer 

monitoring with staff and resources will help achieve these goals.

2. Lack of observations about range expansion and migration of offshore mid-trophic species 

upslope.

3. Changes in schooling fish recommended as mid-trophic selected species above need to be 

assessed, including changes in age distribution and population responses to changing 

climate.

Activity 2.1:

Establish new monitoring of selected midtrophic species in habitats throughout the study 

region, with a focus on locations away from 

anthropogenic factors.

Activity 2.2:

Increase frequency of existing monitoring to 

allow for analysis of the impact of storm events 

on mid-trophic species.

Priority: Priority: 

Current and Potential Partners:

• GFNMS

• PISCO/MARINe

• CalCOFI

• ACCESS

• Point Blue Conservation Science 

• Farallon Institute

• CDFW

• NMFS

• NPS

• California Academy of Sciences

• Local universities, including Sonoma 

State University, San Francisco State 

University, and UC Davis

Current and Potential Partners:

• GFNMS

• PISCO/MARINe

• NPS

• California Academy of Sciences

• Local and statewide universities, 

including Sonoma State University, San 

Francisco State University, UC Santa 

Barbara, and UC Davis

• CDFW

Implementation Timeline:

>1 year

Implementation Timeline:

~1 year

EXISTING MONITORING 

Existing monitoring of selected mid-trophic species is detailed in the table below.

Table 22. Existing monitoring data sources for selected mid-trophic species

MID-TROPHIC SPECIES MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

PISCO/MARINe Pigeon Point, 

Slide Ranch, 

Agate Beach and 

Bolinas Point, 

Chimney Rock, 

Bodega Head

Unspecified Unspecified Monitoring of a 

variety of species 

including CA 

mussel, black & 

red abalone, 

gooseneck 

barnacle, giant 

green and 

sunburst anemone

GFNMS South Farallon 1992 – current 1-3 times per year Monitoring of a 

52
Islands variety of species 

including CA 

mussel, 

Gooseneck 

barnacle, Owl 

limpet, Giant 

Green and 

Sunburst 

anemone

GFNMS and 

CBNMS

Rocky reefs 

throughout Northcentral CA coast

Sporadically Sporadically Species 

inventory, 

density, and 

distribution of 

some selected 

mid-trophic 

species 

ACCESS Cruise 

Data

Cruise lines 2004 – present 3-4 times 

annually, AprilOctober 

Copepods, 

zooplankton, and 

krill; Partnership 

between Point 

Blue 

Conservation 

Science, GFNMS, 

and CBNMS

Bodega Line 

Oceanographic 

Transect

Offshore from 

BML and within 

Tomales Bay

2008 – present Monthly Copepods; 

Available by 

request

Academy Citizen 

Science 

(California 

Academy of 

Sciences and 

GFNMS 

partnership)

Duxbury Reef 

(Bolinas) and 

Pillar Point (Half 

Moon Bay)

2009 – present Monthly as tides 

allow

Rocky intertidal 

invertebrates, 

including 

mussels, Ochre 

sea star, and 

Gooseneck 

barnacle; 

http://www.calaca

demy.org/science/

citizen_science/ro

cky_shore_partne

rship/

GFNMS Longterm Monitoring 

Program and 

Experiential 

Training for 

Students 

(LiMPETS)

Sandy beach and 

rocky intertidal 

habitats within 

the study region

Unspecified Unspecified Rocky intertidal 

and sandy beach 

monitoring of a 

variety of species 

including Mole 

crab, CA mussel, 

Ochre sea star, 

Gooseneck 

barnacle, and 

53
Giant Green and 

Sunburst 

anemone. 

http://limpetsmon

itoring.org/index.

php

NPS San 

Francisco Area 

Network (SFAN) 

Inventory & 

Monitoring

8 National Parks 

within San 

Francisco Bay 

Area

Unspecified Unspecified http://science.natu

re.nps.gov/im/uni

ts/sfan/index.cfm

Fitzgerald Marine 

Reserve docents

Fitzgerald Marine 

Reserve and 

Pillar Point Reef

Unspecified Unspecified Nudibranchs

NMFS Rockfish 

Cruises

Cruise lines off of 

central California

1986 – present Annually in May 

or June

Standardized 

annual midwater 

trawl surveys to 

monitor 

abundance and 

distribution 

patterns of 

young-of-the-year 

pelagic juvenile 

rockfish; 

http://swfsc.noaa.

gov/GroundfishA

nalysis

CDFW Statewide 

Settlement Data

Statewide 20 years Unspecified Statewide

settlement data 

exist with 

UCSB’s Steven 

Schroeter as PI. 

See 

http://dfg.ca.gov/

marine/impact.as

p 

Biological Indicator #3: Spatial Extent of HabitatForming Organisms 

BACKGROUND

The spatial extent of habitat-forming organisms, also 

known as “biogenic habitat,” provides key information 

about changes in habitat availability for other species 

that depend on these resources. Reductions in biogenic 

habitat availability can have large impacts on organisms 

at all trophic levels in the North-central California coast

and ocean region. Beyond providing habitat, 

Figure 8. California Mussels

54
macroalgae, seagrasses, and kelp are also important 

primary producers providing a trophic base to portions of 

the ecosystem food web. As climate change alters the 

physical conditions in the marine environment, it can 

reduce the success of habitat-forming organisms like 

mussels, kelp forests, and seagrasses in areas in which 

they were previously productive.

As with Biological Indicator #2 (mid-trophic level species 

abundance, biomass, and phenology), this indicator is 

intentionally broad to allow the flexibility to choose the 

best possible indicator for relevant habitats within the 

study region. Key habitat-forming organisms to monitor 

are organized by habitat type below:

Table 23. Selected habitat-forming organisms by habitat type

SELECTED HABITAT-FORMING ORGANISMS

ROCKY INTERTIDAL & ISLAND

Mussel beds (Mytilus californianus)

Surfgrass (Phyllospadix scouleri and/or 

Phyllospadix torreyi)

NEARSHORE SUBTIDAL

Bull kelp (Nereocystis luetkeana)

ESTUARIES & BAYS

Pickleweed (Salicornia virginica and/or 

Sarcocornia pacifica)

Eelgrass (Zostera marina)

Cordgrass (Spartina foliosa)

OFFSHORE (ROCKY BENTHIC)

California hydrocoral (Stylaster californicus) 

HABITATS OF INTEREST 

The spatial extent of habitat-forming organisms is a particularly useful indicator where the 

organisms are most frequently found: in rocky intertidal, nearshore subtidal, estuarine, and offshore 

benthic habitats. 

MEASUREMENT 

Techniques for measuring the spatial extent of habitat-forming organisms in the study region vary 

by organism and habitat type and can include overflight transects, percent coverage, and quadrats.

CASE STUDIES FOR MANAGEMENT 

The spatial extent of biogenic habitat can be used by natural resource management in many ways, 

including the following:

• To inform modifications of management strategies that help protect sensitive species 

associated with sensitive biogenic habitats, such as eelgrass beds. 

• To inform decisions about additional restrictions that may be needed on harvesting of 

habitat-forming organisms, including kelp, other macro-algae, and mussels.

• To support planning efforts for wetland restoration projects. 

Figure 9. Seagrass bed along North-central 

California coast 

55
STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 24. Monitoring strategies and activities for habitat-forming organisms

HABITAT-FORMING ORGANISMS MONITORING STRATEGY #1: 

Maintain in situ and aerial monitoring of the spatial extent of habitat-forming organisms.

Need for Additional Funding & Infrastructure: 

$

Gaps in Research:

1. Are there long-term changes in the spatial extent of habitat-forming organisms?

2. Are there changes in the range of habitat-forming organisms?

Activity 1.1:

Maintain funding for existing in situ monitoring of selected habitat-forming organisms.

Priority:

Current and Potential Partners:

• PISCO/MARINe

• Ocean Imaging

Implementation Timeline:

Ongoing

HABITAT-FORMING ORGANISMS MONITORING STRATEGY #2:

Increase in situ and aerial monitoring of the spatial extent of habitat-forming organisms.

Need for Additional Funding & Infrastructure: 

$$$

Gaps in Research:

1. Are changes in the spatial extent of habitat-forming organisms consistent across the region? 

This consistency would allow for increased confidence in conclusions drawn from 

observations.

2. Increased monitoring of habitat-forming organisms is needed in regions that are difficult to 

access via in situ monitoring methods. Remote monitoring provides information about the 

status of many of these regions.

3. Greater knowledge about deep-sea corals in the study region is needed.

Activity 2.1:

Restore funding for aerial 

surveys of the spatial extent of 

habitat-forming organisms.

Activity 2.2:

Increase the number of aerial 

surveys of the spatial extent of 

habitat-forming organisms.

Activity 2.3:

Increase in situ monitoring of the 

spatial extent of habitat-forming 

organisms in key habitats.

Priority: Priority: Priority: 

Current and Potential 

Partners:

• USGS

• CDFW

Current and Potential 

Partners:

• PISCO/MARINe

Current and Potential Partners:

• PISCO/MARINe

• California Academy of 

Sciences

• GFNMS, CBNMS, and 

MBNMS

Implementation Timeline:

<1 year

Implementation Timeline:

>1 year

Implementation Timeline:

~1 year

56
EXISTING MONITORING 

Existing monitoring of the spatial extent of the habitat-forming organisms listed above is detailed in 

the table below. Overall, monitoring is limited and should be expanded. 

Table 25. Existing monitoring data sources for selected habitat-forming organisms

Biological Indicator #4: Seabird Phenology, Productivity, & Diet

BACKGROUND 

Seabird phenology, productivity, and diet provide a year-round picture of health of one category of 

higher trophic levels. It is important to note that seabirds are being used as indicators of higher 

trophic level organisms rather than pinnipeds, sharks, or other apex predators because the species 

listed below are less migratory and can be more effectively and directly linked to changing climate. 

There exist long-term monitoring data for other regionally important apex species such as sharks 

and pinnipeds, collected by universities, NGOs like Point Blue Conservation Science, and agencies 

HABITAT-FORMING ORGANISMS MONITORING - IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

CDFW Aerial 

Surveys

Tomales Bay Unspecified Unspecified Eelgrass

CDFW Aerial 

Surveys

Aerial Survey Unspecified Unspecified Bull kelp and 

Mussel beds

PISCO/MARINe Numerous 

locations in CA 

coast and ocean

Unspecified Unspecified Mussel beds, Bull 

kelp; 

http://data.piscow

eb.org/DataCatal

ogAccess/DataCa

talogAccess.html

Academy Citizen 

Science 

(California 

Academy of 

Sciences and 

GFNMS 

partnership)

Duxbury Reef 

(Bolinas) and 

Pillar Point (Half 

Moon Bay)

Unspecified Monthly as tides 

allow

Extent of mussel 

beds 

http://www.calac

ademy.org/scienc

e/citizen_science/

rocky_shore_part

nership/

San Mateo 

County 

Parks/Tenera

San Mateo 

County coast

1994 – 2004 Unspecified Aerial coverage 

of macroalgae

NOAA Deep Sea 

Coral Cruises

GFNMS, 

CBNMS, 

MBNMS

2010 – present Sporadic, annual 

at most

Deep sea coral

Ocean Imaging 

baseline mapping 

of California 

North-central 

Coast Marine 

Protected Areas

Numerous 

locations in 

North-central 

California coast 

and ocean region

2010 One-time 

baseline dataset

http://oceanspace

s.org/project/nort

h-central-coastnearshore-habitatmapping-usingmultispectralaerial-imagery

57
that include NMFS, and NPS (Crocker et al. 2008; Lee and Sydeman 2009; Allen et al. 2011). 

Monitoring of these additional apex species will likely continue. 

Changes in seabird phenology, productivity, and 

diet can indicate changes in primary productivity. 

Furthermore, simultaneous monitoring of seabird 

phenologies and environmental conditions can 

provide information about potential mismatches in 

species phenology in the North-central California 

coast and ocean region (e.g., Wells et al. 2008). 

Seabird mortality events (as part of seabird 

phenology) can indicate changes in prey, 

atmospheric or oceanic conditions, or the presence 

of harmful algal blooms. Changes in seabird 

productivity can indicate changes in prey 

availability or environmental conditions (Wells et 

al. 2008; Field et al. 2010). Monitoring of seabird 

diet can be used to identify and track changes in 

prey availability (Roth et al. 2007).

Factors beyond anthropogenic climate change that 

can also impact seabird phenology, productivity, 

and diet include changes in human use, 

disturbances, and non-anthropogenic climate 

forcings that impact primary productivity and 

atmospheric or oceanic conditions.

As with Biological Indicators #2 and #3 (midtrophic level species abundance, biomass, and 

phenology and the spatial extent of habitat-forming 

organisms), this indicator is intentionally broad because it provides the flexibility needed to choose 

the best possible indicator for relevant habitats within the study region.

Table 26. Selected seabird species by habitat type

SELECTED SEABIRD SPECIES 

Brandt’s cormorant (Phalacrocorax penicillatus)

Cassin’s auklet (Ptychoramphus aleuticus)

Common murre (Uria aalge)

HABITATS OF INTEREST 

Seabird phenology, productivity, and diet are particularly useful indicators in rocky, nearshore 

subtidal, offshore, and island habitats.

MEASUREMENT 

Seabird Phenology: Seabird phenology is often monitored by tracking the timing of egg laying for 

all selected species, often using seabirds breeding in nesting boxes.

Seabird Productivity: Seabird productivity can be monitored by evaluating the reproductive success 

of each species, as indicated by the number of eggs, hatchlings, and fledglings in seabird nests. 

Figure 10. Brandt’s Cormorant

Figure 11. Common Murre

58
Often, monitoring occurs for seabirds breeding in nesting boxes. Seabird mortality events can also 

be monitored, as this allows for an assessment of post-fledgling success.

Seabird Diet: Seabird diet is often monitored by evaluating the regurgitated meals of seabird chicks, 

direct observations, or recovery of regurgitated pellets. 

CASE STUDIES FOR MANAGEMENT 

Seabird data can be used by natural resource management in many ways, including the following:

• To predict salmon stock abundance using modeled and observed seabird productivity (e.g., 

Roth et al. 2007).

• To identify changes in seabird prey base, as was done during a seabird mortality event in the 

region in 2009. Changes in prey base can have implications beyond seabirds, to other 

species that consume the same prey. Identifying reductions in prey can help management to 

identify vulnerable seabird and other high trophic level species, providing additional 

justification for reducing non-climate stressors on those vulnerable species, such as 

increasing protection or supporting restoration of seabird breeding and roosting sites.

• To identify the onset of a seabird mortality event using baseline and trend monitoring of 

mortality cycles and unusual mortality events.

• To provide an early warning of potential reductions in rockfish population size and 

associated future impacts on higher trophic level species, through monitoring of common 

murre diet and phenology, particularly delayed egg laying. 

STRATEGIES AND ACTIVITIES TO ACHIEVE MONITORING GOALS

Table 27. Monitoring strategies and activities for seabirds

SEABIRD MONITORING STRATEGY #1: 

Maintain monitoring of seabird diet and abundance as an indicator of changes in prey availability 

and primary productivity.

Need for Additional Funding & Infrastructure: 

$

Gaps in Research:

1. A better understanding of the causes behind seabird diet variability, which cannot be fully 

explained by large-scale climate indicators, is needed.

2. Changes in seabird prey availability need to be tracked.

3. Continued observations of the locations of nesting colonies are needed to ensure that any 

potential shift in the distribution of nesting colonies is identified.

Activity 1.1:

Continue to monitor seabird diets on the 

Farallon Islands, Año Nuevo Island, and rocky 

shore habitats.

Activity 1.2:

Continue to monitor seabird species abundance, 

both on land and at sea, through in situ and atsea surveys.

Priority: Priority: 

Current and Potential Partners:

• Point Blue Conservation Science

• US Fish and Wildlife Service (USFWS)

• NPS

• Audubon Society

• Oikonos

• CDFW

Current and Potential Partners:

• GFNMS, CBNMS, and MBNMS

• Farallones Marine Sanctuary Association 

(FMSA)

• Point Blue Conservation Science

• USFWS

• NPS

59
• Sea Ranch CCNM Stewardship Task 

Force

• BLM

• Bureau of Ocean Energy Management

(BOEM)

• OST

• USGS-WERC

• Audubon Society

• Oikonos

• CDFW

• UC Santa Cruz

• Sea Ranch CCNM Stewardship Task 

Force

• Stewards of the Coast and Redwoods

• BLM

• USGS-WERC

Implementation Timeline:

Ongoing

Implementation Timeline:

Ongoing

SEABIRD MONITORING STRATEGY #2:

Increase monitoring of seabird phenology to provide information about the impacts of potential 

changes in upwelling on higher trophic level species.

Need for Additional Funding & Infrastructure: 

$$$

Gaps in Research:

1. An increased understanding of changes in upwelling and their impacts on high trophic-level 

species is needed.

2. The impacts of harmful algal blooms, storm events, prey availability, and pathogens on 

seabirds need to be better tracked.

Activity 2.1:

Survey seabird phenology, especially the timing of breeding and causes of mortality, in key 

habitats.

Priority:

Current and Potential Partners:

• FMSA

• Point Blue Conservation Science

• NPS

• USFWS

• USGS

• CDFW

• Oikonos

• PFEL

• OST

Implementation Timeline:

Ongoing

SEABIRD MONITORING STRATEGY #3:

Maintain monitoring of seabird productivity in key habitats, as defined by seabird reproductive 

success (number of eggs, hatchlings, and fledglings).

Need for Additional Funding & Infrastructure: 

$

Gaps in Research:

1. The impacts of climate change on seabird productivity, which can provide insight into 

potential changes in other high trophic-level species productivity, need to be tracked.

Activity 3.1:

60
Continue to monitor seabird productivity in key habitats, particularly on the Farallon Islands and 

Año Nuevo Island.

Priority:

Current and Potential Partners:

• GFNMS

• NPS

• USGS

• USFWS

• CDFW

• California State Parks

• Point Blue Conservation Science

• UC Santa Cruz

• Oikonos

Implementation Timeline:

Ongoing

EXISTING MONITORING 

Existing monitoring of selected seabird species is detailed in the table below. Overall, seabird 

monitoring could be expanded and analyzed to help meet the monitoring objectives.

Table 28. Existing monitoring data sources for selected seabird species

SEABIRD PHENOLOGY MONITORING – IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

GFNMS and 

FMSA 

BeachWatch

42 shoreline 

locations in study 

region

1993 – present Every 2 weeks Abundance and 

distribution of 

seabirds

Point Blue 

Conservation 

Science

Southeast 

Farallon Island

1969 – present Every 1-7 days Variety of 

species, info 

available at: 

http://www.point

blue.org/ourscience-andservices/conserva

tionscience/oceansandcoasts/farallonislandsresearch#seabirds

USFWS Point Reyes, 

Devils Slide

1996 to present Every 1-7 days

CDFW Office of 

Spill Prevention 

and Response 

Seabird Health 

Study

Unspecified, but 

based in Santa 

Cruz, CA

Unspecified Unspecified http://www.dfg.ca

.gov/ospr/Science

/marine-wildlifevetcare/SeabirdH

ealth.aspx

61
SEABIRD PRODUCTIVITY MONITORING – IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

Point Blue 

Conservation 

Science

Southeast 

Farallon Island

1969 – present Every 1-7 days Variety of 

species, info

available at: 

http://www.point

blue.org/ourscience-andservices/conserva

tionscience/oceansandcoasts/farallonislandsresearch#seabirds

Oikonos Año 

Nuevo Island 

Restoration 

Project

Año Nuevo 

Island

1996 – present Unspecified http://www.anonu

evoisland.org/pag

e/about-1

Marin Audubon 

Christmas Bird 

Count

Point Reyes and 

Bolinas Lagoon

Varies by 

location

Annual http://www.marin

audubon.org/chris

tmas-birdcount.php

CDFW-UC Santa 

Cruz

Aerial Survey Unspecified 1-2 times a month Patchy 1994-1997

USFWS Point Reyes, 

Devils Slide

1996 to present Every 1-7 days

SEABIRD DIET MONITORING – IN SITU DATA:

DATA SOURCE LOCATION OR 

GRID SIZE

DATE RANGE FREQUENCY COMMENTS

Point Blue 

Conservation 

Science

Southeast 

Farallon Island

1969 – present Every 1-7 days Variety of 

species, info 

available at: 

http://www.point

blue.org/ourscience-andservices/conserva

tionscience/oceansandcoasts/farallonislandsresearch#seabirds

USFWS Point Reyes, 

Devils Slide

1996 – present Every 1-7 days

62
Summary and Conclusion

Given the strong scientific consensus about anthropogenic climate change and the observed and 

projected global and regional impacts of this change (Bindoff 2007; Largier et al. 2010 and sources 

therein), natural resource managers in the North-central California coast and ocean region are 

actively planning for climate change. The physical and biological ocean climate indicators 

presented in this monitoring inventory and plan (Figures 1 and 2) provide vital information about 

the presence and impacts of climate change on the ecosystems within the region, which extends 

from Point Año Nuevo to Point Arena (Figure 4). They were specifically developed to support 

science-based decision making at local, state, and federal agencies, and they are the first regional 

ocean climate indicators developed by the National Marine Sanctuary System.

The indicators were developed at Gulf of the Farallones National Marine Sanctuary (GFNMS) over 

the course of the two-year, highly interdisciplinary and collaborative Ocean Climate Indicators

Project. A core project team consisting of sanctuary managers and federal and university research 

scientists developed the indicator selection criteria and an initial set of candidate ocean climate 

indicators. The selection criteria were based on those developed by the National Research Council 

(NRC 2000), and they assessed each candidate indicator’s ability to answer priority management 

questions, its link to climate change, and its relative statistical strength. A much larger group of 

more than 50 regional research scientists and natural resource managers provided input about how 

well a refined set of candidate indicators met the selection criteria in an Indicator Selection Survey. 

Of the survey respondents, 36 participated in the Indicator Selection Workshop, where smaller 

groups of natural resource managers and research scientists used the survey results to inform 

conversations about the relative merits of each candidate indicator and selected a smaller number of 

finalist ocean climate indicators. Indicators that were recommended by at least three of the four 

breakout groups were taken to represent a consensus. As a result, the ocean climate indicators in 

this document represent the consensus of over 50 regional research scientists and managers, and 

they provide the best-available information about the impacts of climate change on the ecosystems 

of the North-central California coast and ocean region. 

Following the indicator development process, the GFNMS Advisory Council approved the 

formation of a working group to incorporate the indicators into a monitoring inventory and plan. 

The resulting Indicators Working Group consisted of a subset of 13 Ocean Climate Indicators 

Project collaborators from a broad cross-section of disciplines and expertise, including research 

scientists from universities and NGOs, and managers from many of the federal and state agencies 

with jurisdiction in the region. The working group met in a series of three meetings with the 

objectives of developing an indicator-based climate change monitoring goal for the region, 

discussing the best-available physical and biological indicator observations, determining selected 

species for biological indicators, and developing monitoring strategies and activities for each 

indicator to meet the monitoring goals and objectives. For these selected species there is a clear, 

scientifically accepted mechanism by which climate change can alter their distribution or 

abundance, and monitoring is already available in some portions of the North-central California 

coast and ocean region. 

63
The Indicators Working Group has identified several overarching indicator monitoring 

recommendations:

1. Continued and/or expanded financial support for ongoing indicator monitoring is vital for 

science-based climate change decision-making because it allows for identification of longterm, climate-scale changes in the region’s ecosystems.

2. Synthesis of existing regional climate change research is key to ensuring that monitoring is 

as efficient and useful as possible.

3. There is a need for increased communications with regional and local government agencies 

to ensure that natural resource managers have access to the information, partners, and 

resources that they need to assess and reduce their vulnerability to climate change.

Specific monitoring strategies and activities are also suggested for each ocean climate indicator in 

this document. Broadly speaking, these strategies are centered on maintaining existing indicator 

monitoring, and expanding or establishing new monitoring in critical habitats. To maximize the 

utility of these indicators for decision-makers, priority levels, current and potential future partners, 

funding requirements, and implementation timelines are provided in tables for each indicator 

monitoring strategy. 

The Indicators Working Group recognizes that regular evaluations of and updates to the Ocean 

Climate Indicators Monitoring Inventory and Plan are key to ensuring that the recommended 

indicators are scientifically sound and relevant to regional decision-makers. Ongoing evaluation of 

the indicators may result in the development of indicator benchmarks like those available for 

ecological indicators in the San Francisco Bay Estuary (SFEP 2011), further increasing their utility 

to decision-makers. The Indicators Working Group recommends that the Ocean Climate Indicators 

Monitoring Inventory and Plan be updated by GFNMS in two ways:

1. On an annual basis, GFNMS staff should consider updating data sources for each indicator.

2. Every 5 years, the GFNMS SAC should consider convening a working group to review the 

indicators contained in this report, to re-evaluate their utility to managers and their ongoing 

scientific relevance, and to consider adding any new indicators that reflect advances in 

scientific understanding of climate change in the North-central California coast and ocean 

region.

Moving forward, the Indicators Working Group also recommends that the indicators be integrated 

into a web-based indicator decision support tool, for which additional financial support would be 

needed. Such a tool would provide quick and easy access to pre-processed, pre-screened, and preinterpreted indicator observations and available pre-existing indicator projections that are produced 

by other researchers. Increasing decision-maker access to interpreted ocean climate indicator 

monitoring and projections, and ensuring that long-term, consistent indicator monitoring exists, are 

key to ensuring that the best-available science is informing decisions in order to maximize the 

resiliency of the North-central California coast and ocean region. In addition, financial support is 

needed at GFNMS, other government agencies, and partner institutions and organizations to 

maintain and expand indicator monitoring.

64
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66
List of Acronyms

Acronym Full Name

ACCESS Applied California Current Ecosystem Studies

AVHRR Advanced Very High Resolution Radiometer

BLM Bureau of Land Management

BML Bodega Marine Laboratory

BOAR Bodega Ocean Acidification Research

BOEM Bureau of Ocean Energy Management

BOON Bodega Ocean Observing Node

CalCOFI California Cooperative Oceanic Fisheries Investigations

CBNMS Cordell Bank National Marine Sanctuary

CCS California Current Ecosystem

CDIP Coastal Data Information Program

CDFW California Department of Fish and Wildlife

CeNCOOS Central and Northern California Ocean Observing System

CO2 Carbon Dioxide

CO-OPS Center for Operational Oceanographic Products and Services

CSFR2 Climate System Forecast Reanalysis, v2

DIC Dissolved Inorganic Carbon

DO Dissolved Oxygen

ENSO El Niño Southern Oscillation

FMSA Farallones Marine Sanctuary Association

GFNMS Gulf of the Farallones National Marine Sanctuary

GHRSST Group for High-Resolution Sea Surface Temperature

IOOS United States Integrated Ocean Observing System

LiMPETS Long-term Monitoring Program and Experiential Training for Students

MARINe Multi Agency Rocky Intertidal Network

MBARI Monterey Bay Aquarium Research Institute

MBNMS Monterey Bay National Marine Sanctuary

MODIS Moderate Resolution Imaging Spectroradiometer

NARR North American Regional Reanalysis

NASA National Aeronautics and Space Administration

NCAR National Center for Atmospheric Research

NCEP National Centers for Environmental Prediction

NDBC National Data Buoy Center

NGO Non-governmental Organization

NMFS National Marine Fisheries Service

NOAA National Oceanic and Atmospheric Administration

NOS National Ocean Service

NPGO North Pacific Gyre Oscillation

NPS National Park Service

NWS National Weather Service

OA Ocean Acidification

OCOF Our Coast–Our Future

OMEGAS Ocean Margin Ecosystems Group for Acidification Studies

67
OMZ Oxygen Minimum Zone

ONMS Office of National Marine Sanctuaries

OSCAT Oceansat-2 Scatterometer

OST California Ocean Science Trust

PACE Postdocs Applying Climate Expertise

PaCOOS Pacific Coast Ocean Observing System

PDO Pacific Decadal Oscillation

PISCO Partnership for Interdisciplinary Studies of Coastal Oceans

PMEL NOAA Pacific Marine Environmental Laboratory

POES Polar-orbiting Operational Environmental Satellites

QuickSCAT NASA Quick Scatterometer

RTC Romberg Tiburon Center 

SAC Sanctuary Advisory Council (NOAA GFNMS and CBNMS)

SFAN NPS San Francisco Area Network

SSS Sea Surface Salinity

SST Sea Surface Temperature

SWFSC Southwest Fisheries Science Center

UC University of California

UCAR University Corporation for Atmospheric Research

USFWS US Fish and Wildlife Service

USGS US Geological Survey

VIIRS Visible Infrared Imaging Radiometer Suite

WERC Western Ecological Research Center

68
Report Photo and Figure Credits

Figure Description Credit

Cover photo, 

left

Shoreline along North-central California coast NOAA GFNMS 

BeachWatch

Cover photo, 

middle

Brandt’s cormorant Chad King, 

MBNMS

Cover Photo, 

right top

San Francisco tide gauge NOAA Tides and 

Currents

Cover photo, 

right middle

Bull kelp Steve Lonhart, 

MBNMS

Cover photo, 

right bottom

Gopher rockfish Chad King, 

MBNMS

Figure ES-1 Scientist sampling phytoplankton NOAA MBNMS

Figure ES-2 Juvenile blue rockfish Steve Lonhart, 

MBNMS.

Figure ES-3 Surfgrass Steve Lonhart, 

MBNMS.

Figure ES-4 Brandt’s cormorant Jason Thompson, 

NOAA GFNMS 

BeachWatch

Figure ES-5 Map of study region (thick red lines), with related 

sanctuary boundaries (black solid lines) and proposed 

sanctuary expansion areas (black dashed lines) 

Tim Reed, GFNMS

Figure ES-6 Shoreline along North-central California coast NOAA GFNMS 

BeachWatch

Figure 1 Physical ocean climate indicators for the North- central 

California coast and ocean region

Benét Duncan

Figure 2 Biological ocean climate indicators for the North-central 

California coast and ocean region

Benét Duncan

Figure 3 Ocean Climate Indicators Project flowchart Benét Duncan

Figure 4 Map of study region (thick red lines), with related 

sanctuary boundaries (black solid lines) and proposed 

sanctuary expansion areas (black dashed lines)

Tim Reed, GFNMS

Figure 5 Annual maximum air temperature at Southeast Farallon 

Island from 1971 – 2012. The diagonal black line 

illustrates a linear regression indicating the trend in the 

data.

Point Blue 

Conservation 

Science, 

unpublished data

Figure 6 Giant green anemone NOAA GFNMS 

BeachWatch

Figure 7 California mussels Steve Lonhart, 

MBNMS.

Figure 8 Seagrass bed along North-central California coast NOAA GFNMS 

BeachWatch

Figure 9 Brandt’s cormorant Chad King, 

MBNMS

Figure 10 Common murre Dru Devlin, NOAA 

GFNMS/ACCESS

69
Appendix A: Climate Change Priority Management Questions

Note: These questions are based on the 2008 Condition Report and on the updated ONMS 

Condition Report questions.

As a result of climate variability and change (as outlined in the Ecosystem Description and 

Conceptual Ecological Model):

1. What is the integrity of major habitat types and how is it changing? That is, are there 

changes in the extent of habitat available to organisms or in the quality of that habitat, 

whether it is non-living or biogenic?

2. Have water conditions changed? Conditions include all potential impacts of climate change 

on water, including temperature, acidity, sea level, upwelling, storminess, erosion, 

sedimentation, and freshwater delivery, and the cascading effects of these impacts.

3. What is the status of biodiversity, most especially the functional interactions between 

species? How is it changing?

4. What is the status and health of keystone and foundation species, and how is it changing? 

Changes in the status and health of either type of species can affect ecosystem structure and 

integrity through changes in the abundance of dependent species.

5. What is the status and health of key species and how is it changing? 

6. What is the status of non-indigenous species, and how is it changing? That is, is the 

recruitment, establishment, or severity of impacts of non-indigenous species changing?

Definitions:

Biogenic Habitat – Habitat whose presence is due to the growth of animals or plants which create 

substrates and floating habitats that attract or support other organisms.

Key Species – Species of particular interest from the perspective of sanctuary management. May 

not be abundant or provide high value to ecosystem functioning, but their presence and health is 

important for the provision of sanctuary services. Key species include those targeted for special 

protection, those with specific regulations to minimize perturbations from human disturbance, 

indicator species, and “flagship” species.

Keystone Species – Species on which the persistence of a large number of other species in the 

ecosystem depends. Their impact is important at the community or ecosystem level. Keystone 

species can include habitat creators like corals and kelp; predators that control food web structure 

like sea otters and Humboldt squid; and herbivores that regulate benthic recruitment like certain sea 

urchins.

Foundation Species – Single species that define much of the structure of a community by creating 

locally stable conditions of other species, and by modulating and stabilizing fundamental ecosystem 

processes. Foundation species have a higher abundance than keystone species. In the GFNMS, they 

include krill, kelp, rockfish, coral, and mussels.

70
Appendix B: Indicator Selection Criteria & Post-Assessment Questions

Note: The indicator selection criteria presented below:

1. Is based on the peer-reviewed work presented in the National Research Council’s 

“Ecological Indicators for the Nation” report, and in the San Francisco Estuary 

Partnership’s “State of the San Francisco Bay 2011” report.

2. Was used as the basis of the Indicator Survey, which was sent to Ocean Climate Indicator 

Workshop participants.

Selection Criteria:

1. General importance:

a. Does indicator tell about changes in important attributes due to changes in climate?

b. Will changes in the indicator result in an identifiable change in the system?

c. Can it inform direct or indirect actions by sanctuary management?

d. Is the indicator compatible with those being developed by other groups in the region?

e. Is it based on the GFNMS ecosystem description (see above)?

2. Temporal and spatial scales of applicability

a. Can indicator detect changes at appropriate temporal and spatial scales? 

3. Statistical properties of indicator data:

a. Is the available indicator data good enough in accuracy, sensitivity, precision, and 

robustness?

b. Is it insensitive to changes in monitoring technology?

c. Can it detect signals above “noise” of other environmental variation?

4. Reliability:

a. Has past experience with indicator demonstrated its reliability?

b. If not, is there other historical evidence that is reliable?

5. Data requirements:

a. Does enough information exist to develop reliable indicator measurements?

b. Can new information be collected to develop reliable indicator measurements?

c. What is required for indicator to detect a trend?

d. Would another dataset provide sufficient information about this indicator? That is, 

are proxies available? 

6. Necessary skills:

a. Can the indicator be easily monitored without extensive training, or does it require 

specialized knowledge?

Additional Assessment Questions:

1. Data requirements:

a. What new data, if any, needs to be collected to monitor the indicator?

b. Are historical datasets available for this indicator?

c. Where is existing indicator available? Can we use it?

2. Costs, benefits, and cost-effectiveness:

a. What are the clear benefits of using this indicator?

b. What are the costs of obtaining data for the indicator?

c. Do the benefits of using this indicator exceed the cost of obtaining data?

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Appendix C: Gulf of the Farallones Regional Ecosystem Description

All information included in the Ecosystem Description is excerpted from the Gulf of the Farallones 

National Marine Sanctuary’s 2010 Condition Report and 2008 Management Plan, with the 

exception of the Nearshore Subtidal Habitat discussion, and all sections on Potential Impacts of 

Climate Change, which are excerpted from the 2010 Gulf of the Farallones and Cordell Bank 

National Marine Sanctuaries Climate Change Impacts Report.

General Overview 

Physical Setting

The project study region extends along the North-central California coast from Point Arena in the 

north to Point Año Nuevo in the south, and offshore along the continental slope at the western 

boundaries of the Cordell Bank, Gulf of the Farallones, and Monterey Bay National Marine 

Sanctuaries. The North-central California coastline includes sandy beaches, rocky cliffs, open bays 

(including Bodega and Drakes Bays), enclosed bays or estuaries that are open to the ocean yearround (Bolinas Lagoon, Tomales Bay, and Bodega Harbor), and seasonally closed lagoons (Esteros 

Americano and de San Antonio). Six general habitat types exist within the study region: Sandy 

Beaches, Rocky Intertidal, Nearshore Subtidal, Estuaries and Bays, Islands, and Offshore. 

Subsequent sections will describe each habitat type in depth. 

This region contains the widest portion of the continental shelf on the west coast of the United 

States. Here, the gently sloping continental shelf extends westward nearly 57km from the California 

coast, with an average depth of approximately 120m. A thin layer of generally coarse sediments 

surrounds patches of rocky outcroppings at the shelf break and the continental slope.

The Farallon Islands are located along the outer edge of the continental shelf, approximately 48km 

to the west of San Francisco. Consisting of 7 islands and large rocks, they are part of a larger 

submarine ridge that includes South, Middle, and North Farallon Islands, Hurst Shoal, Fanny Shoal, 

Noonday Rock, Rittenburg Bank, and Cordell Bank. The variable bathymetry along Farallon 

Escarpment is associated with significant ecological richness, high species diversity, and spawning 

and feeding areas. 

Physical Processes

Water circulation within the study region is dominated by the California Current, which travels 

southward along the west coast of the United States. In this wind-driven upwelling system, 

northerly winds during spring and summer months drive a shallow surface layer, which travels 

offshore due to the Coriolis Effect. This offshore movement of surface water is also known as 

Ekman Transport. Deep, cold, nutrient-rich water move upwards to replace the surface water lost 

along the coastline, and it creates a food-rich environment that promotes the growth of organisms at 

all levels of the marine food web. 

During relaxation periods, the prevailing northerly winds weaken, causing currents to flow to the 

north and halting upwelling. Relaxation periods can occur during spring and summer, but weakened 

winds are typical during the fall season. As a result, water temperatures increase during fall months, 

and warm, lower-salinity waters move onshore. 

Winter months are characterized by rain-bearing cold fronts that pass through the study region. 

Winds are typically from the west and south, which contributes to northward surface currents and 

72
downwelling over the continental shelf. The northward-traveling California Undercurrent comes to 

the surface.

Sediments are transported throughout the study region by currents year-round. As a result, seasonal 

deposition and erosion of sediments change the width and steepness of beaches from season to 

season. For example, sediments are washed into the region by rivers and from shoreline erosion 

during the winter storm season. Esteros become closed off from the ocean during summer and fall 

by seasonally formed sand bars. At the same time, beach sand is moved downcoast by longshore 

drift.

Habitat #1: Sandy Beaches

Physical Setting

Sandy beaches are mostly located along the coastal border of the study region. Five distinct zones 

within sandy beach habitat are defined by the level of tidal inundation: The upper intertidal beach 

zone has a short inundation time, while the mid-littoral beach zone has a moderate inundation time. 

The swash zone is located where waves break along the beach and is submerged for approximately 

12 hours daily. The low intertidal beach zone has a long inundation time and is exposed to nearconstant wave action, while the surf zone is submerged continuously and exposed to constant wave 

action.

Physical Processes and Components

Sandy beach habitat constantly changes due to the influence of waves on each of the five zones, 

with a wide temperature range due to changing wave action and tidal exposure.

Biological Processes and Components

The species distribution within sandy beach habitat is strongly influenced by the physical factors 

listed above, which can vary between zones. Food and shelter are provided by detached plant and 

algal debris, and by corpses of fishes, seabirds, and marine mammals, especially in upper intertidal 

beach zones. Sandy beaches are home to numerous invertebrate communities, and they are breeding 

grounds for birds and pinnipeds.

Potential Impacts of Climate Change

Sea level rise and increased erosion are expected to intensify pressure on sandy beaches, 

particularly in mid and upper beach zones, which can in turn impact the biota, biodiversity, and 

food web in this habitat. Sand dunes may need to retreat landward. Shorebirds that live in sandy 

beaches could face lower availability of invertebrate prey, reduced macroalgae wrack, and habitat 

loss. Fish and pinnipeds could lose habitat that they depend on for reproduction.

Habitat #2: Rocky Intertidal (aka Rocky Shore)

Physical Setting

Rocky intertidal habitat consists of rocky areas found between high and low tide water levels. It 

covers approximately 22% of the shoreline in the Gulf of the Farallones National Marine Sanctuary 

and can be found at Bodega Head and Duxbury Reef.

Physical Processes and Components

Frequent wave action, changing tide levels, and wind have strong impacts on rocky intertidal 

habitat, causing drying and heating/cooling during low tide.

73
Biological Processes and Components

Organisms living in rocky intertidal habitats must survive extreme physical conditions that change 

rapidly, and their distribution is influenced by tidal inundation and wave exposure. Coralline algae 

provide cover and food for a diverse array of marine invertebrates that include barnacles, limpets, 

black turban snails, mussels, sea anemones, and sea urchins. Different fish are common at different 

depths within rocky intertidal habitats, but they include rockfish, Cabazon, and small surfperches. 

Pinnipeds also breed along rocky shores (see the Islands section for more details).

Potential Impacts of Climate Change

Climate change-induced increases in average water and air temperature, prevalence of extreme 

events, ocean acidification, and changes in upwelling patterns, are of primary concern in rocky 

intertidal habitats. Most organisms there are ectothermic, and changes in ambient temperatures 

could cause an increased susceptibility to disease, population declines, and even mass mortality of 

some organisms. Upwelling can bring increasingly acidic waters to intertidal organisms, decreasing 

the ability of calcifying organisms to produce shells, and altering the delivery of food, nutrients, and 

larvae to intertidal habitats. Rising sea level will pressure organisms to migrate if upland habitat is 

available. Increased wave activity is expected to alter the temperature and physical forces that 

intertidal organisms experience. Populations of larval and adult organisms may respond to the wide 

array of climate change-induced pressures by shifting their ranges.

Habitat #3: Nearshore Subtidal (aka Shallow Subtidal)

Physical Setting

Nearshore subtidal habitat can be found at depths up to 30-50m, below the tide line, where coastal 

habitat meets the mainland. The seafloor there is often described either as sandy continental shelf or 

as rocky reef.

Physical Processes and Components

Upwelling plays an important role in delivering cool, nutrient-rich water to nearshore subtidal 

habitat. Shallow depths allow for good light penetration, while runoff and precipitation provide 

freshwater input, especially during the winter storm season.

Biological Processes and Components

Kelp forests are located in many of the rocky reef zones within nearshore subtidal habitat. Common 

kelp species include Macrocystis and Nereocystis. These kelp forests provide a home for other 

organisms like Black Rockfish, which in turn provide a food source for seabirds and pinnipeds. 

Dislodged kelp provides a critical food resource to sandy beach, intertidal, and deep-water offshore 

habitats. In addition, calcifying organisms, benthic macroalgae, phytoplankton, larvae, and spores 

are all found within nearshore subtidal habitat.

Potential Impacts of Climate Change

Changes in upwelling, stratification, and offshore transport could impact the delivery of nutrients 

from deep and offshore waters to nearshore subtidal habitat, and could also affect the dispersion of 

larvae and spores. Increased ocean acidification would affect the shell thickness and survival of 

calcifying organisms. Rising sea level would decrease the amount of light available in bottom water 

layers, which could cause a shoreward migration of nearshore subtidal habitat. At the same time, 

increasing sea level could also alter the substrate composition and the shape of the shoreline, which 

would reduce the amount of land available for a shoreward migration. Increased storminess 

associated with climate change could increase wave heights, which in turn could alter sediment 

74
redistribution and coastal topography. Increased precipitation and runoff associated with more 

frequent storminess would increase freshwater input, while increased turbidity and light attenuation 

could decrease the growth of kelp. In addition, increased storminess would likely cause an increase 

in the dislodgement of kelp holdfasts, which would further the loss of kelp forests within nearshore 

subtidal habitat. 

Habitat #4: Estuaries and Bays

Physical Setting

Estuaries and bays are mostly small and sandbar-built within the study region. Examples of small 

estuaries include Bolinas Lagoon, Estero Americano, and Estero de San Antonio. Tomales Bay is a 

moderately sized bay, and San Francisco Bay is a major estuary located outside of the study region, 

but with important impacts on the region.

Physical Processes and Components

Small estuaries are often built with the seasonal inflow of sediments that are transported by coastal 

ocean circulation. They are protected from the open ocean, and as a result, bays and estuaries 

typically have shallow, warm water with good light penetration. Tributaries provide high nutrient 

input.

Biological Processes and Components

The combination of warm temperatures, abundant light, and high nutrient levels makes estuaries 

and bays a highly productive habitat type. A variety of ecosystems can be found within this habitat, 

including mudflats, brackish water, eelgrass beds, salt marshes, and tidal creeks. Mudflats contain a 

high concentration of burrowing organisms like clams, snails, worms, and crabs, which in turn 

provide a food source for shorebirds and wading birds. Eelgrass beds are home to juvenile stages of 

coastal fish, and pacific herring, and they provide a place for invertebrates to spawn and feed.

Estuaries and bays also provide a feeding, spawning, and nursery area for fish that include Pacific 

herring, smelt, starry flounder, sharks, rays, and surfperch. Low-level carnivores of invertebrates

and planktivores are the most common fish in estuaries and bays. There is higher abundance and 

species richness during summer, when young marine species invade these habitats. Coho salmon, a 

federally threatened species, travel from the ocean through bays and estuaries, and they depend on 

this habitat for reproduction.

Over 180 species of birds have been observed on the beaches between Bodega Head and the 

northern border of Santa Cruz County. Within estuaries and bays, shorebirds probe the shore to feed 

on buried clams, worms, crustaceans, and small fishes. Commonly seen birds include black 

oystercatchers, dowitchers, sandpipers, herons, ducks, rails, and geese. The black rail is a California 

threatened species with rapidly diminishing numbers in its habitat in Tomales Bay and Bolinas 

Lagoon. It is now rarely seen in salt marshes in the region. In addition, populations of sea lions and 

seals haul out and reproduce in Drakes Estero, Bolinas Lagoon, and Tomales bay.

Potential Impacts of Climate Change

Sea level rise due to changing climate is expected to impact estuaries and bays differently, 

depending on the ability of an estuary to migrate inland and upward, and its reliance on organic 

versus inorganic deposition. The potential loss of estuarine intertidal mudflats could have a large 

effect on shorebirds and harbor seals. Increased interannual variation of watershed outflow may 

favor invasive species and alter the salinity gradient. Increased air and water temperatures may put 

75
greater stress on some plants and animals, magnify pathogen and parasite problems, and favor the 

range expansion of other plants and animals. Increasing atmospheric carbon dioxide causes an 

increase in ocean acidity, which strongly impacts estuaries because freshwater input reduces their 

ability to buffer acidic ocean inflow. Acidification of estuarine waters decreases animal fertilization 

and embryo development, and it can cause shell dissolution in juvenile bivalves. Changes in 

currents and atmospheric circulation may alter the transport of organisms within and between 

estuaries.

Habitat #5: Islands

Physical Setting

Island habitats within the study region include the Farallon Islands and Año Nuevo Island. See the 

General Overview for more details.

Physical Processes and Components

The Farallon Islands and Año Nuevo Island are isolated, rocky habitats that provide remote 

breeding and feeding areas away from intense human activities.

Biological Processes and Components

Marine productivity is extremely high in the waters surrounding the Farallon Islands. As a result, a 

diverse assemblage of invertebrates, fish, seabirds, and marine mammals has been observed there. 

The Farallon Islands are home to the largest concentration of nesting seabirds within the contiguous 

United States. Over 300,000 seabirds nest on the islands annually from May-July, and 11 of 16 

breeding seabird species along the US Pacific coast have colonies there. Common aquatic birds 

include waterfowl and shorebirds like black oystercatchers, pelicans, loons, and grebes.

Island habitat is also an important location for breeding populations of northern fur seals, elephant 

seals, harbor seals, California sea lions, and Steller sea lions. One of the last California populations 

of federally threatened Steller sea lions lives in the study region. The Farallon Islands lie in the 

southern part of the species’ range, and the population has decreased there by 80% over the past 50 

years. A small breeding colony of fur seals has lived on the Farallon Islands since 1996, after not 

being seen there for the prior 176 years. The California sea lion is the most conspicuous and widely 

distributed pinniped in the study region, where it can be found year-round. The population of 

California sea lions increases by 8-12% yearly. The northern elephant seal is the largest pinniped 

species in the study region. Approximately 20% of the harbor seals in California breed in the 

sanctuary.

Potential Impacts of Climate Change

Increased sea level could significantly alter island habitats and cause a redistribution of wildlife 

populations as organisms are forced to move upland or abandon flooded areas. Intensified winter 

precipitation and increased rainfall may increase erosion of hillsides and cause flooding of lowlying areas, which would in turn degrade nesting habitat and alter vegetation structure. Rising 

average air temperatures could also alter vegetation and stress wildlife within island habitats.

Habitat #6: Offshore

Physical Setting

Offshore habitats can be subdivided into three distinct zones: pelagic shelf, pelagic slope, and 

offshore benthic (which includes submarine canyons). The pelagic shelf and slope zones consist of 

water above the seafloor of the continental shelf and slope, respectively. Waters in the pelagic shelf 

76
zone range in depth from 0-200m, and the pelagic slope zone occurs where the depth of the seafloor 

rapidly increases from 200-2000m. The pelagic zones often contain newly upwelled water, with 

some warmer water in retention zones, plume-influenced water from San Francisco Bay, and surf 

zone water near the surface. In the deep-sea pelagic zone, there is generally low light, cold water 

temperature, and high pressure. In the deep-sea portions of the pelagic zone, there is generally low 

light, cold water temperature, and high pressure. Benthic habitat contains the seafloor, which can 

vary by depth and region. Along the continental shelf, the substrate can be sandy or rocky, with a 

nearly continuous blanket of mud up to 30m thick found at depths from 40-90m. The seafloor along 

the continental slope typically has a soft bottom with some rocky outcroppings, except along 

submarine canyons, which have steep, rocky walls with complex physical structures that hold 

sediments.

Physical Processes and Components

Along the continental shelf (in the offshore benthic zone), wave action and subsurface currents 

cause shifting sediments that consist of varying combinations of sand, silt, and clay. During high 

wave action along the continental shelf, substrate that had previously settled can be resuspended and 

transported offshore. Kelp forests within the pelagic shelf zone alter turbulent flow patterns due to 

the large size and high density of kelp. Because of the depth of the pelagic slope zone, organisms 

there are exposed to extremely low light, cold temperatures, and very high pressure.

Biological Processes and Components

In all offshore habitat zones, white sharks, turtles, and cetaceans are present. The study region has 

one of the largest known concentrations of white sharks in the world, with a stable, genetically 

isolated population of 175-299 adults. White sharks arrive nearshore during summer months, near 

pinniped haul-out and breeding colonies between Point Año Nuevo, the Farallon Islands, Tomales 

Point, Point Reyes, and Bodega Headlands. They leave during winter months to migrate southward 

to the central Pacific and the Hawaiian Islands. White sharks are an apex predator, which means 

that they are a key species. Their removal could have cascading trophic impacts on the population 

dynamics of their prey, and on the food web as a whole.

Turtles are also seasonally present in offshore habitats where they forage on jellyfish. They follow 

warmer waters during summer and fall, and their location is greatly influenced by the timing of the 

relaxation of upwelling winds. Leatherback turtles are observed annually in the study region, while 

other species are rarely seen. 

There are 12 regularly seen species of cetaceans in offshore habitats. Minke whale, harbor porpoise, 

Dall’s porpoise, and Pacific white-sided dolphin are all observed year-round, while gray, 

humpback, and blue whales are observed seasonally. The study region is a nursery for harbor 

porpoise and Pacific white-sided dolphins, and a major migration route for gray whales from 

December-March. From April-November, offshore habitats are a destination feeding and migration 

route for humpback and blue whales. In fact, the study region has one of the largest concentrations 

of both gray and humpback whales in the northern hemisphere. In addition, offshore seabirds such 

as Sooty Shearwaters consume small schooling fish, squid, and zooplankton in the highly 

productive California Current waters. 

Offshore pelagic shelf zones contain nearshore kelp beds, which support juvenile finfish, pinnipeds 

(especially harbor seals and Steller and California sea lions), birds, and occasionally gray whales. 

Below 60ft, kelp growth is limited due to a lack of light. Two species of krill, which are the 

keystone invertebrate species for the entire study region, are based in the offshore continental shelf. 

77
Thysanoessa spinifera is a coastal species, and it is dominant during summer months when 

upwelling is relaxed. Euphausia pacifical is an oceanic species, and it is dominant during the late 

winter and spring upwelling season. Productive commercial fisheries are also found here, with the 

location and composition dependent on oceanographic conditions. Pelagic shelf zones along the 

study region coastline also retain larval and juvenile salmon, northern anchovy, rockfish, and 

flatfish, which reduces pressure on these fishes and ensures their continuing populations. 

Organisms found in the offshore pelagic slope zone are specialized for high pressure, low oxygen, 

and low light. Some adapt to produce their own light with bioluminescence. Organisms here depend 

on surface-level primary production. Common invertebrates include coralline algae, brittle stars, 

and serpulid worms. Productive commercial fisheries are located in offshore continental slope 

zones, where rockfish, thornyfish, sablefish, and Dover sole are found.

In offshore pelagic zones, there is a diverse and complex food web that consists of plankton, 

invertebrates, fishes, sea turtles, birds, and mammals. Fish species vary with migration and 

spawning, but they include predatory finfish, northern anchovy, Pacific mackerel, and market squid 

nearshore, and juvenile finfish in kelp beds. Deep-sea pelagic invertebrates like jellies, squids, 

octopuses, barnacle larvae, copepods, and shrimp are slow growing and eat less frequently. 

Benthic zones with sandy substrate along the continental shelf contain animals that live in tubes and 

burrows (i.e. clams, crustaceans, and mollusks), and shrimp, prawns, flatfish, and Dungeness crabs. 

Benthic zones with rocky substrate along the continental shelf contain extensive macroalgae, 

abalones, sea urchins, rockfishes, surfperches, and Cabazon. The seafloor along the continental 

slope is home to deep-sea pelagic invertebrates like cold-water corals, sea anemones, worms, snails, 

clams, barnacles, copepods, and crabs. The rocky walls of offshore submarine canyons are home to 

species like flatfishes and invertebrates like polychaete worms, mollusks, shrimp, and brittle stars.

Potential Impacts of Climate Change

Changes in upwelling and stratification due to climate change can affect nutrient delivery to 

offshore pelagic shelf and slope habitats. Reduced nutrient delivery and primary productivity 

(decreased zooplankton and phytoplankton) could have a large impact cascading through the entire 

ecosystem. Increasing water temperatures will pressure some organisms to shift their geographic 

range northward, and will alter reproductive rates and the timing of growing seasons for others. 

Reduced numbers of some species, like juvenile rockfish, during breeding times for common 

seabirds can cause mass mortality events. As in other habitats, ocean acidification is likely to result 

in decreased calcification rates of calcifying organisms, including shell-building pteropods and 

foraminifera that are key to ocean food webs. Reduced numbers of calcareous organisms, combined 

with warming temperatures, could allow gelatinous organisms like jellyfish to increase in size and 

population. Increased ocean storminess, wave activity, and turbidity can negatively impact kelp 

growth, which could reduce the available feeding and breeding grounds for a variety of fish, 

seabirds, cetaceans, and pinnipeds.

78
Appendix D: Conceptual Ecological Model for North-central California Coast 

and Ocean 

79
Appendix E: Priority Levels of Indicator Monitoring Strategies 

Indicator monitoring activities with “critical” priority levels are identified in the table below. While 

all indicator monitoring activities were carefully selected and continued funding for these activities 

is important, “critical” priority activities are those for which funding is critical, even during times of 

limited financial resources because they can capture more critical information about climate change 

impacts more efficiently than “very important” and “important” priority activities. 

Indicator Monitoring 

Activity Brief Description Page #

Physical Indicators

#1: Air Temperature Activity 1.1 Continued support for air temperature 

monitoring at weather stations

12

#2: Alongshore Wind Speed 

and Direction

Activity 1.1 Maintain wind data collection 16

#2: Alongshore Wind Speed 

and Direction

Activity 1.2 Repair/replace damaged offshore wind 

sensors 

16

#3: SST Activity 1.1 Continued support for SST monitoring 18-

19

#5: DO Activity 1.1 Add oxygen sensors to existing moorings 

and surveys

26-

27

#6: Ocean Chemistry Activity 1.1 Add pH and CO2 instruments to existing 

moorings and offshore cruises

29

#7: Wave Height and Direction Activity 1.1 Continued support for existing wave 

monitoring, including on buoys

31-

32

#8: Sea Level Activity 1.1 Sustained resources for long-term sea 

level monitoring

35

Biological Indicators

#1: Primary Productivity Activity 1.1 Continued support for existing chlorophyll 

monitoring

37-

38

#2: Mid-Trophic Level Species 

Abundance, Biomass, and 

Phenology

Activity 1.1 Maintain current mid-trophic species 

monitoring

41-

42

#3: Spatial Extent of HabitatForming OrganismsActivity 1.1 Maintain support for existing in situ 

monitoring of habitat-forming organisms

47

#4: Seabird Phenology, 

Productivity, and Diet

Activity 1.1 Continue monitoring of seabird diets on 

islands and rocky shore habitats

50-

51

#4: Seabird Phenology, 

Productivity, and Diet

Activity 1.2 Continue monitoring of seabird abundance 

on land and at sea

50-

51

#4: Seabird Phenology, 

Productivity, and Diet

Activity 3.1 Continue monitoring of seabird 

productivity in key habitats

52

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Appendix F: Promising Mid-Trophic Level Species

Some mid-trophic level species (Biological Indicator #2), which would provide valuable 

information if long-term datasets were underway or already available, have been designated as 

promising species and are provided below:

PROMISING MID-TROPHIC LEVEL SPECIES

ROCKY INTERTIDAL

Purple sea urchin (Strongylocentrotus 

purpuratus)

Owl limpet (Lottia gigantea)

Black (Haliotis cracherodii) & Red (Haliotis 

rufescens) abalone 

Nudibranch (Nudibranchia)

ESTUARIES & BAYS

Large annelid (Polychaeta)

Goby (Gobiidae) 

OFFSHORE (BENTHIC & PELAGIC)

Krill (Euphausiacea)

Gelatinous zooplankton (Gelata)

Foraminifera (Foraminifera)

81