San Francisco Bay 

Subtidal Habitat Goals Report

Conservation Planning for the Submerged Areas of the Bay

50-Year Conservation Plan • 2010

California State Coastal Conservancy and Ocean Protection Council

NOAA National Marine Fisheries Service and Restoration Center

San Francisco Bay Conservation and Development Commission

San Francisco Estuary Partnership
 i

contributors

Inter-Agency Staff

Natalie Cosentino-Manning, Marine Habitat Restoration Specialist, NOAA 

Restoration Center

Brenda Goeden, Dredging and Regional Sediment Management Manager, Bay 

Conservation and Development Commission

Judy Kelly, Director, San Francisco Estuary Partnership

Marilyn Latta, Project Manager, State Coastal Conservancy

Korie Schaeffer, Northern California Habitat Coordinator, NOAA National 

Marine Fisheries Service,, Habitat Conservation Division

Caitlin Sweeney, Deputy Director (emeritus), Bay Conservation and 

Development Commission

Consultants

Sebastian Araya, Lead GIS Analyst and Developer, Stillwater Sciences

Sarikka Attoe, Laboratory Technician, University of California at Davis

Patrick J. Balducci, Senior Economist, Battell–Pacific Northwest National 

Laboratory

Erin Beller, Environmental Analyst, San Francisco Estuary Institute

Dr. Katharyn Boyer, Associate Professor, San Francisco State University

Kristen Cayce, GIS Manager, San Francisco Estuary Institute

Dr. Andrew Cohen, Director Biological Invasions Program, San Francisco 

Estuary Institute

Caitlin Coleman-Hulbert, Laboratory Technician, University of California at 

Davis

Dr. Edwin T. Grosholz, Professor, University of California at Davis

Robin Grossinger, Senior Scientist, San Francisco Estuary Institute

Jennifer Hunt, Environmental Analyst/ Project Manager, San Francisco Estuary 

Institute
﻿ii • San Francisco Bay Subtidal Habitat Goals Report

Dr. Wim Kimmerer, Research Professor, San Francisco State University

Marcus Klatt, GIS Analyst, San Francisco Estuary Institute

Aroon Malwani, Associate Environmental Scientist, San Francisco Estuary 

Institute

Eric Polson, P.E., Civil Engineer, Eric Polson Engineering

Dr. Christine Werme, Independent Consultant, Berkeley CA

Dr. Sandy Wyllie-Echeverria, Research Scientist, Friday Harbor Lab, University 

of WA

Dr. Chela Zabin, Ecologist, UC Davis and Smithsonian Environmental Research 

Center

Editorial Assistance

Lisa Owens Viani, Public Outreach Coordinator, San Francisco Estuary 

Partnership

Graphic Design

Seventeenth Street Studios, Oakland CA

printing

JT Litho, Oakland CA
 iii

acknowledgments

T he completion of this Subtidal Habitat Goals Report would 

not have been possible without the help and dedication of a number 

of individuals. We would first like to thank the numerous members of 

the public and the local, state, and federal agency personnel who attended our 

workshops and meetings to discuss the development of the project and who 

provided written comments on early drafts of the Report. Mary Selkirk and 

her colleagues at the Center for Collaborative Policy were invaluable during 

the initial stages of gathering input from agency personnel and interested 

stakeholders, and throughout the project provided expert facilitation of 

meetings for the administrative core group, committees, and public workshops. 

Administrative core group members are the heart of this project and spent 

countless hours on planning, research, outreach, and content development. 

They include Natalie Cosentino-Manning, Brenda Goeden, Judy Kelly, Marilyn 

Latta, Korie Schaeffer, and Caitlin Sweeney. Project Manager Marilyn Latta 

provided solid leadership and a strong knowledge of bay restoration, and kept 

the process moving, with more than 75 contributors to the Report. Science 

advisor Dr. Wim Kimmerer provided a sound scientific basis for planning, 

and helped us to focus the scope and scientific direction, and to incorporate 

adaptive management into the Report’s priorities. In addition, thorough and 

constructive executive reviews were provided on numerous drafts by Steve 

Edmonson, Judy Kelly, Patrick Rutten, Sam Schuchat, and Will Travis.

The diligent work to compile existing subtidal GIS information for the maps 

was started by Dan Robinson, former NOAA Fellow at the Bay Conservation 

and Development Commission, and completed by Charleen Gavette, GIS 

Specialist for the National Marine Fisheries Service, Southwest Region. Graphic 

artist Cleo Vilett created all of the conceptual diagrams, using the University of 

Maryland Integration and Application Network symbol library. Graphic artist 

Tim Gunther created the artistic image of subtidal habitats. 

We also sincerely appreciate the support and input received from our science, 

management, restoration, and executive steering committee members. Please 

see the list of members in Appendix 1-1. These dedicated and knowledgeable 

individuals include experts in biology, botany, fisheries, invertebrates, hydrology, wetlands, geology, engineering, contaminants, policy, restoration, management, and other fields related to subtidal habitats. Many of these committee 
﻿iv • San Francisco Bay Subtidal Habitat Goals Report

members have participated since the inception of this project in 2001, and have 

tirelessly provided valuable input and their best scientific advice even in the 

face of multiple gaps in data. We truly value their time and input to the Project, 

and especially their review of multiple drafts over the past couple of years.

Staff members from the various lead and partner agencies provided critical 

assistance in identifying partners and data, and ensuring that current local, 

state, and federal efforts were taken into consideration as new recommendations for subtidal areas were developed. Several people were integral to 

the establishment of this project, including Jim Bybee, Abe Doherty, Michelle 

Jacobi, Katie McGourty, and Brian Mulvey. We would also like to particularly 

thank many agency staff and consultants who gave of their time and expertise, including Natalie Badrei, Christina Cairns, Tim Doherty, Zooey Diggory, 

Naomi Feger, Gary Greene, Michelle Jesperson, Jaime Kooser, Adrienne 

Harrison, Amy Hutzel, Moira McEnespy, Rebecca Smyth, Rebecca Pollack, 

Christina Hoffman, Laura Hoberecht, Brian Ross, Ariel Ambruster, Tina 

Chen, Paula Trigueros, and Megan Wood. Science writer Ellie Ely helped 

write the Appendix report on Anthropogenic Alterations in San Francisco 

Bay. Additional members of the public and industry representatives provided 

invaluable feedback and written comments, particularly Jim McGrath, Ellen 

Johnck, Bill Butler, Barry Keller, Mike Hanson, and James Haussener.

Photographs in the report were graciously provided by a number of individuals. Special gratitude goes to photographers Greg and Kim Lorenz, who took 

the underwater images of the bay. Craig Ponsford and Diana Benner offered 

boat and kayak support to take these photographs, and Corbin Pagter longboards to get into shallow areas. 
 v

contents

Contributors i

Acknowledgments iii

Chapter One Purpose of and Need for a Subtidal Habitat Goals Report 1

Chapter Two Planning Decisions and Considerations 15

Chapter Three Science and Cross-Habitat Goals for All Subtidal Habitat Types 33

Chapter Four Soft-Bottom and Other Mobile Substrates 53

Chapter Five Rock Habitats 73

Chapter Six Artificial Structures 81

Chapter Seven Shellfish Beds 93

Chapter Eight Submerged Aquatic Vegetation 115

Chapter Nine Macroalgal Beds 141

Chapter Ten Integrated Restoration 147

Chapter Eleven Implementation 163

References 171

Photo Credits 179

Appendices can be found on disk, inside back cover. The appendices, report, 

and interactive versions of the maps can be found at www.sfbaysubtidal.org.

1-1 Project Methodology

1-2 SF Bay Economic Evaluation Report 

1-3 Anthropogenic Alterations in SF Bay

1-4 Glossary of Terms

2-1 Habitat Stressor Narrative Descriptions

2-2 Effects of Climate and Other Long-Term Changes on Subtidal Habitats 

6-1 Creosote and Artificial Structures Assessment

7-1 Shellfish Opportunities and Constraints Report

8-1 Eelgrass Opportunities and Constraints Report 

CEQA Determination

The Subtidal Goals document is statutorily and categorically exempt from the California Environmental Quality Act (CEQA), for the reasons presented below.

The Subtidal Goals Project will result in documents that provide information, recommendations 

and goals for protection, restoration, appropriate use, and research to improve the subtidal habitats in San Francisco Bay. The project involves data collection, resource evaluation, and planning; 

all of these activities are exempt under CEQA. The documents that are prepared for the Subtidal 

Goals Project will not have a legally binding effect on later activities of public agencies.

 The portions of the Subtidal Goals Project that consist of basic data collection and resource 

evaluation activities are categorically exempt from CEQA review, under 14 CCR Section 15306 

(“Information Collection”). The information-collecting activities will be implemented in a manner that will not result in a serious or major disturbance to an environmental resource.

 The portions of the Subtidal Goals Project that involve planning are statutorily exempt pursuant to Public Resource Code Section 21102 and 14 CCR Section 15262 (“Feasibility and Planning Studies”) since they are for possible future actions that have not been approved, adopted, 

or funded. The planning studies will include consideration of environmental factors, to avoid 

impacts to sensitive environmental resources.

EFFECTS OF THE PROJECT

The Subtidal Habitat Goals Project will result in a recommendations document that is intended 

to provide general technical assistance and discretionary guidance for managing San Francisco 

Bay subtidal habitats. The document will result in no direct or indirect effects on resources of 

concern as outlined in the National Environmental Policy Act (NEPA) checklist. Implementation 

of specific recommendations or goals identified in the document will undergo individual NEPA 

analysis, as necessary.

NEPA DETERMINATION

After reviewing the project in relation to NAO 216-6, including the criteria on the NEPA 

checklist, and review by the Southwest Regional NEPA Coordinator, NOAA concluded that 

the proposed action would not have a significant effect, individually or cumulatively, on the 

human environment. Further, NOAA determined that the proposed action may appropriately 

be categorically excluded from the requirement to prepare either an environmental assessment 

or environmental impact statement, in accordance with Categorical Exclusion 6.03.c.3(i) Other 

Categories of Actions Not Having Significant Environmental Impacts. More specifically, this 

action represents guidance of an administrative, technical, or procedural nature, the environmental effects of which are too broad, speculative, or conjectural to lend themselves to meaningful analysis, and will be subject later to the NEPA process, either collectively or case-by-case.

San Francisco Bay Subtidal Habitat 

Goals Project

Website: www.sfbaysubtidal.org

Email: info@sfbaysubtidal.org

Please find photo credits on 

page 179.

©2010 State Coastal Conservancy

State Coastal Conservancy

1330 Broadway, Suite 1300

Oakland, CA 94612

510-286-1015
Executive Summary • S-1

EXECUTIVE SUMMARY

S

an francisco bay is one of the largest estuaries on the West Coast 

and one of the most important both for the habitat it provides for fish 

and wildlife and for the many benefits and opportunities it offers people. 

Its natural beauty gives the Bay Area the iconic identity for which it is known 

throughout the world, while its waters ensure an enviable climate and quality 

of life for over 7.5 million residents. Residents commute across the bay on 

ferries, or enjoy it while boating, fishing, swimming, windsurfing, and birding 

in and around its waters. Visitors from around the country and world are 

drawn to this heart of the Bay Area as well, adding millions of dollars each 

year to the local and state economies. The bay is a busy center of commerce: 

cargo ships and tankers from around the Pacific Rim depend on its ports and 

infrastructure, and approximately two million tons of sand are mined from 

beneath its surface each year for use in construction. Historical oyster shell 

deposits are mined for livestock and chicken feed, soil conditioner, and as a 

dietary supplement for human consumption. 

In addition to offering these aesthetic, economic, and recreational values, the 

bay supports a critical food web. Herring and Dungeness crab, among many 

other species of fish and shellfish, rear in its waters while sturgeon, salmon, 

and steelhead feed and rest in the bay during their migrations to and from its 

San Francisco Bay 

Subtidal Habitat Goals Report

Conservation Planning for the Submerged Areas of the Bay
S-2 • San Francisco Bay Subtidal Habitat Goals Report

rivers and streams and the ocean. Its vast open water, sloughs, rivers, streams, 

and tidelands host millions of migratory birds every year as they move up and 

down the Pacific Flyway, as well as provide habitat for numerous resident water, 

shore, and song birds. The bay also provides important habitat for marine 

mammals, shellfish, and aquatic invertebrates—the smaller, often unseen but 

important inhabitants of the estuarine ecosystem.

Looking Beneath the Surface

Subtidal habitat is a critical piece of this ecosystem. Subtidal habitat, as defined 

in this report, includes all of the submerged area beneath the bay’s water surface: mud, shell, sand, rocks, artificial structures, shellfish beds, eelgrass beds, 

macroalgal beds, and the water column above the bay bottom. Although this 

hidden underbelly of the bay is often thought of as a featureless mud bottom, 

its unique habitats provide diverse three-dimensional structures, including 

sand waves more than three meters high. Its eelgrass and shellfish beds act as 

ecosystem engineers and provide substrate for reproduction and food resources 

for species such as herring and salmon; rocky outcrops offer substrate for seaweeds and invertebrates; mixed sediments in shoals and channel banks are 

used by a variety of species. Many shellfish, macro- and micro-invertebrates, 

fish, marine mammals, diving ducks, and other wildlife feed, rest, hide, and 

reproduce in subtidal areas. Large populations of shorebirds feed on the estuary’s subtidal and intertidal mudflats. 

The bay also supports a variety of indirect ecosystem services, including nutrient cycling, climate regulation, flood protection, water quality maintenance, 

and sediment transport. The Subtidal Habitat Goals Report recommends 

preserving and restoring the bay’s subtidal resources for their ecosystem 

functions and habitat values as well as for their ecosystem services to humans. 

The vision statement and goals presented in the report were developed using 
Executive Summary • S-3

the best available science in the interest of supporting, maintaining, and 

improving upon these ecosystem functions, values, and services. 

Report Audience and Use

Along with the Baylands Ecosystem Habitat Goals Project and the Uplands 

Habitat Goals Project, the San Francisco Bay Subtidal Habitat Goals Project 

(Subtidal Goals Project) represents a milestone in regional habitat planning for 

San Francisco Bay and its watersheds. Bay Area planners and resource managers now have a comprehensive and innovative ecosystem-based management 

vision for a continuum of habitat types from the bottom of the bay to tidal wetlands and grassland transition zones to upland areas.

The Subtidal Goals Project report is neither a policy nor a regulatory document. It is designed to give resource managers, regulatory agencies, environmental groups, researchers, industry, and anyone interested in this important 

bay habitat the basic information they need to plan conservation, restoration, 

research, and protection activities related to subtidal habitat in the San Francisco Estuary. 

Implementation of the goals in the report will occur through a number of 

avenues: local governments may incorporate these recommendations into their 

planning processes and documents. Non-profits may use the report when seeking funding for restoration or management projects, and researchers may wish 

to refer to it for guidance in writing proposals. Regulatory agencies may use 

this report to evaluate, revise, or implement their policies. However, new policies or modifications to existing policies proposed on the basis of this report 

will require a separate process in which each agency will analyze recommended 

policies in the context of its existing authorities and public input process.

The Subtidal Goals Project is a collaboration among the San Francisco Bay Conservation and Development Commission (BCDC), California Ocean Protection 

Council (OPC)/California State Coastal Conservancy (SCC), the National Oceanic and Atmospheric Administration (NOAA), and the San Francisco Estuary 

Partnership (SFEP). Lead staff from those agencies worked with the broader scientific community, managers, restoration practitioners, and stakeholders over several years to develop the goals set forth in this document. More about the process 

used to develop the project can be found in Appendix 1-1.

NOAA, BCDC, SFEP, and SCC each have different authorities, mandates and 

policies regarding conservation and management of subtidal habitats. As such, 

each agency may choose to use this document in different ways.

•	 While this document does not supersede or change NOAA authorities or 

mandates, NOAA staff may reference information in this document when 

implementing consultations pursuant to the Endangered Species Act and 

the Essential Fish Habitat provisions of the Magnuson-Stevens Fishery 

Conservation and Management Act. 

Bay Area planners and 

resource managers now 

have a comprehensive and 

innovative ecosystembased management vision 

for the bottom of the bay to 

tidal wetlands and grassland transition zones to 

upland areas.
S-4 • San Francisco Bay Subtidal Habitat Goals Report

•	 NOAA may reference this document when evaluating research priorities 

both for NOAA Science Centers and other scientific entities.

•	 The NOAA Restoration Center may use this document to help prioritize 

restoration projects for funding and support.

•	 San Francisco Bay Conservation and Development Commission staff 

may use this document as background when considering future revisions 

to the San Francisco Bay Plan and may reference it when evaluating 

proposed projects under BCDC’s existing regulatory authority over 

development in and around San Francisco Bay.

•	 The San Francisco Estuary Partnership may reference this document 

when implementing the Comprehensive Conservation and Management 

Plan for San Francisco Bay, in seeking federal dollars for San Francisco 

Bay conservation, and in selecting restoration and/or research projects

to fund.

•	 The State Coastal Conservancy may use this document to identify 

acquisition opportunities, prioritize conservation and strategic planning, 

and develop restoration projects to support and fund. The Ocean 

Protection Council may utilize the document in making decisions and 

prioritizing research areas, especially as they relate to issues of land-sea 

interactions, ecosystem research, and climate change planning.
Executive Summary • S-5

Planning Framework and Approach

The Subtidal Goals Project takes a bay-wide approach to setting science-based 

goals for maintaining a healthy, productive, and resilient ecosystem. The vision 

statement of the project is to achieve a net improvement of the subtidal ecosystem in San Francisco Bay through science-based protection and habitat 

restoration. Where possible, these subtidal goals are designed to connect with 

intertidal habitats and with goals developed by other projects, including goals 

for baylands and uplands habitats. Unlike in the Baylands Goals effort, historical information about subtidal habitat is lacking. Thus the goals set forth in 

this document do not attempt to restore the bay to historical conditions but are 

designed to improve the condition of the subtidal ecosystem. The baseline for 

the project is 2010, and the planning horizon is 50 years. 

Collecting and mapping baseline geospatial data of all of the subtidal habitat 

types was a critical piece of this project. Maps of habitat distribution, ownership, and stressors for each habitat type—as well as proposed restoration sites 

for native oysters and eelgrass and pilot locations for intertidal sand beaches 

and living shorelines—are presented throughout the report.

Early in the process, the following key planning decisions were made:

•	 The geographic scope of the Subtidal Goals Project is San Francisco Bay 

from Sherman Island west to the southern extent of the bay and seaward to 

the Golden Gate (Point Bonita to Point Lobos). Although the SacramentoSan Joaquin Delta is not included in the project scope, conditions in the 

delta and their relationship to subtidal habitat in the bay are addressed in 

the sections on freshwater input and climate change (see Chapter 3).

•	 For the purposes of this project, “subtidal habitat” includes all submerged 

areas of the bay. The project also includes certain intertidal habitats that 

were not specifically addressed in the 1999 Baylands Ecosystem Goals 

Report: intertidal mudflats, eelgrass, sand beaches, rocky intertidal and 

subtidal areas, and artificial substrate.

•	 The report uses a precautionary approach, erring on the side of 

conserving and protecting resources. 

•	 Available information about existing conditions serves as a baseline.

•	 The goals build upon opportunities and information developed by 

existing subtidal pilot projects, including in-the-water monitoring, 

restoration, mitigation, and research projects in San Francisco Bay.

•	 This document avoids setting priorities among habitats although 

restoration of some may result in conversion of others: for example, 

some soft substrate may be lost or enhanced through restoration of 

eelgrass or shellfish beds.

The vision statement of the 

project is to achieve a net 

improvement of the subtidal 

ecosystem in San Francisco 

Bay through science-based 

protection and habitat 

restoration. 
S-6 • San Francisco Bay Subtidal Habitat Goals Report

•	 Because there is a great deal of uncertainty about the functions and 

value of subtidal habitats and the utility and likely success of restoration, 

this report recommends using an adaptive management approach in 

implementing the goals. 

•	 As part of adaptive management, progress on achieving the goals—as 

measured by improved scientific understanding and practical experience 

in subtidal habitat restoration and protection—should be reviewed and 

evaluated in a report by 2020. The goals can then be modified as needed. 

Interim updates on particular topics can be provided within 10 years, and 

discussed at regional forums and conferences.

Establishing the Goals

Goals for each of the subtidal habitats are based on the vision statement and 

the following foundational science goals: 

•	 Understand the value of the habitats

•	 Understand the interactions among habitats

•	 Understand the long-term prospects for subtidal habitats

•	 Develop mechanisms for adapting to climate change

Cross-Habitat Goals were also developed in response to four issues—invasive 

species, oil spills, marine debris, and public access/awareness—that affect all 

subtidal habitats:

•	 Minimize the impacts of aquatic invasive species on native subtidal 

habitats in San Francisco Bay. 

•	 Protect San Francisco Bay from both acute and chronic oil spills.

•	 Prevent and capture land or marine sources of trash before they enter 

the bay.
Executive Summary • S-7

•	 Identify, prioritize, and remove large sources of marine debris from 

intertidal and subtidal areas of the bay.

•	 Increase public awareness and foster support for subtidal habitat 

protection.

Taking into account the extent of scientific understanding of each habitat each 

goal was then vetted through a decision tree. That process led to establishing 

specific habitat goals and actions in one of four broad directions: 

•	 Enhancing, creating, or restoring particular habitats

•	 Protecting habitats 

•	 Observing habitats, taking no action

•	 Eliminating habitats

Other key conclusions reached after vetting each habitat through the decision 

tree include:

•	 Subtidal to intertidal mudflats support valued services and are under 

various threats from human activities and climate change. Opportunities 

for restoration are based on uncertain techniques, so this report 

emphasizes protecting habitat and applying restoration methods 

experimentally.

•	 Muddy soft-bottom habitat is essential for some species and probably 

supports the most known ecosystem services of any habitat. Although it 

is plentiful, several threats exist. However, there are few opportunities for 

restoration, leading to an emphasis on protection.

•	 Sand bottom is used for sand mining, but little is known about its role 

in non-extractive ecosystem services. This lack of knowledge leads to 

a recommendation to protect existing sand resources while pursuing 

research into the impacts of sand mining and the value of this habitat 

type to species and ecosystem services. 
S-8 • San Francisco Bay Subtidal Habitat Goals Report

•	 Rock outcrops support ecosystem services and are under threat, but 

restoration would be logistically difficult and therefore unlikely; the 

report thus recommends protection actions only.

•	 Artificial structures support valued ecosystem services but also can 

impair others. Since they are artificial, most of them cannot be considered 

to be in short supply, nor are they under threat. Conversely, there is 

interest in removing some of them, especially derelict structures no 

longer in use, leading to an expansion of other more favored habitats.

•	 Several habitats (e.g., eelgrass, oyster beds) have clear benefits in 

supporting valued ecosystem services, although the degree of support is 

uncertain. They are likely in short supply and under various threats, and 

restoration has been successful at small scales. Therefore restoration goals 

are the principal focus for these habitats, although protection goals are 

also necessary. 

•	 Algal beds support ecosystem services (although at a small scale), but 

they can also be nuisances under some conditions. Because it is unknown 

whether and which species of algal beds are under threat or in short 

supply, the decision tree process led to identifying research goals only.

•	 The water column forms the background for all of the other habitats. It 

supports all ecosystem services. Its existence is not threatened, but water 

quality could become degraded. However, as discussed in Chapter 3, 

water quality is the province of various agencies and is not addressed in 

this project.
Executive Summary • S-9

Habitat Snapshots

Science, protection, and restoration goals were developed for the following six 

subtidal habitats:

1. Soft Substrate. More than 90% of the estuary’s bottom is composed of 

particles small enough to be moved by tidal currents. Soft-bottom habitat 

includes the soft substrate, organisms living on or within the substrate, 

and the overlying water column. This habitat is threatened by construction 

activities, deposition of material from dredging and sand mining, wakes 

from ships and ferries, and a variety of contaminants, including some 

toxic “hot spots.” Soft-bottom habitat may also be threatened by an overall 

decrease in sediment supply from upstream, and by sea-level rise. The 

report therefore recommends that the quality of this habitat be improved 

and that it be managed properly.

2. Rock. Relatively little hard substrate occurs naturally in the estuary. Rock 

habitat encompasses boulders to bedrock; i.e., rock that is not normally 

moved by currents. Shellfish beds and some algal beds are a subset of 

rock habitat. This habitat is threatened by blasting for navigational safety, 

colonization by invasive species, possibly by sediment deposition, and 

in the case of intertidal rock, from oil spills and trampling. While rock 

habitats support valued ecosystem services and are in short supply in 

the estuary, restoration seems impractical. The Subtidal Goals Project 

recommends protecting and managing rock habitat from being removed 

for vessel traffic and damaged by public access, and enhancing it by 

removing invasive species and debris. It also recommends improving 

scientific understanding of the ecosystem services this habitat provides 

and the species that use it.

3. Artificial Structures. Artificial structures are found throughout the estuary 

and include a wide variety of human-built objects designed to protect 

shorelines and shoreline structures and for transportation, recreation, and 

more recently, restoration (oyster shell and artificial reefs). While artificial 

structures support some valued ecosystem services, they are not in short 

supply, and they can have some detrimental effects. The Subtidal Goals 

Project recommends further study of the advantages and disadvantages 

of removing abandoned pier pilings, and if removal is decided upon, that 

it be done using an adaptive management approach. It also recommends 

using a pilot project approach, and if creosote pilings are removed, 

providing eelgrass as a substitute substrate for attracting spawning 

herring. Goals for artificial structures focus on protecting the habitat 

values of existing actively-used structures, removing and preventing 

structures that harm the subtidal system, and improving understanding 

of the role of these structures in the subtidal system.

Rock

Soft Substrate

Artificial Structures
S-10 • San Francisco Bay Subtidal Habitat Goals Report

4. Shellfish Beds. Hard-bottom shellfish beds are locations where a shellfish 

species occupies more than 50% of an area of more than a few square 

meters. Five species of shellfish occur in San Francisco Bay: native 

Olympia oysters, California mussels, hybridized Bay mussels, and 

non-native ribbed horsemussel and green bagmussels (the latter two 

are not considered in this report). Small populations of the non-native 

Pacific oyster are found in the South Bay, where eradication efforts are 

underway. The Olympia oyster is the most abundant and the only species 

that is a native confined to estuaries. Numerous individuals have been 

found on hard substrates in the Central Bay and to a lesser extent in San 

Pablo and the South Bays. Native oysters are threatened by high rates 

of sedimentation and extended periods of low salinity. Human-induced 

threats include water pollution, boating, shipping, and dredging, which 

can disrupt oyster beds or cause sediment to smother the beds. The 

Subtidal Goals Project recommends building upon the demonstration 

oyster restoration work that has been performed to date, and moving 

toward larger-scaled pilot projects while focusing on knowledge gained 

in the process (adaptive management). Goals for shellfish beds include 

protecting existing native oyster beds, creating and enhancing additional 

beds, and improving scientific understanding of ecosystem services, 

factors influencing the beds, and restoration methods.

5. Submerged Aquatic Vegetation. The term “submerged aquatic vegetation” 

(SAV) refers to all underwater flowering plants. In the San Francisco 

Estuary, SAV includes sago pondweed (Stuckenia pectinata, formerly 

Potamogeton pectinatus), eelgrass (Zostera marina), and other species of 

seagrass, including the surfgrasses (Phyllospadix torreyi and P. scouleri), 

and widgeongrass (Ruppia maritima). Several freshwater plant species, 

mostly introduced, are found mainly in the delta (e.g., the Brazilian 

waterweed Egeria densa, an invasive nuisance species) and are outside 

of the geographic scope of this project. In San Francisco Bay, eelgrass 

is much more extensive than other SAV, and its role and restoration 

potential are understood better than for other SAV (Appendix 8-1). The 

largest eelgrass beds in the estuary are in shallow subtidal regions of San 

Pablo Bay and Richardson Bay, with smaller beds scattered in shallow 

areas mainly between Carquinez Strait and Hayward. The largest bed 

in the bay is located between Point San Pablo and Point Pinole, and 

contains about half of the total acreage. Threats to SAV in San Francisco 

Bay include activities associated with shipping and boating, which can 

disrupt seagrass beds directly through destruction of plants by boat 

propellers, anchors and anchor chains, dredging, and construction of 

facilities (e.g., docks, harbors, breakwaters, ports). Indirect effects arise 

through increased suspended sediments due to dredging and boat wakes, 

or shading from structures such as docks. Hardening of the shoreline can 

reflect waves, increasing wave action and limiting or destroying beds. 

Most of these threats apply to eelgrass in the San Francisco Estuary but 

Submerged Aquatic Vegetation

Shellfish Beds
Executive Summary • S-11

are focused in localized areas. Impacts from dredging seem to have a 

limited spatial and temporal effect; damage from boat anchors, shoreline 

development, and ship wakes is also likely to be localized. Oil spills can 

inundate and smother eelgrass beds, particularly those in the intertidal or 

shallow subtidal zones. Eelgrass beds may respond to rising sea level by 

establishing closer to the present-day shoreline and dying out at greater 

depths. The dwindling sediment supply to the estuary may decrease 

turbidity, allowing eelgrass to grow at greater depths but possibly also 

promoting competing blooms of phytoplankton.

The restricted extent of eelgrass beds may limit their support of valued 

ecosystem services. Restoration has been demonstrated to be feasible 

although questions remain about the anticipated trajectory of restoration 

and associated response of ecosystem functions and services. Restoration 

is warranted for eelgrass beds, but should be done within an experimental 

framework.

6. Macroalgal Beds. Four species of macroalgae—Ulva spp., Gracilaria 

pacifica, Fucus gardneri, and the introduced Sargassum muticum—are 

sufficient to create beds in the estuary; however, their distribution and 

extent is poorly known. Macroalgae provide a suitable food source for 

a variety of grazers, predominantly macroinvertebrates. Water birds use 

it to line their nests. The beach wrack produced by macroalgae is an 

important food source for invertebrates living in beaches, mudflats, and 

marshes: they in turn provide food for shorebirds and other species along 

the shore. There have been few reports of nuisance blooms of macroalgae 

in the bay, although this could change if turbidity decreases. Intertidal 

algal beds are vulnerable to trampling and recreational harvesting as 

well as oil spills and dispersants. Because it is unclear whether additional 

macroalgal beds would be beneficial in the bay or that they are in short 

supply, and because it is difficult to distinguish algal beds that support 

ecosystem services from those that interfere with them, the Subtidal 

Goals Project recommends that additional research be performed and 

existing macroalgal beds protected.

Macroalgal Beds
S-12 • San Francisco Bay Subtidal Habitat Goals Report

The Science Goals1

Three key principles governed the establishment of science goals for subtidal 

habitats:

•	 Acknowledge key gaps in the knowledge needed for decisions about 

the value of restoration, and for effective protection and restoration. 

Substantial gaps are addressed by the following research questions:

Which ecosystem services do the target habitats support, and how?

What is the relationship between quantity of the habitat and the amount or 

value of those ecosystem services?

What interactions (conflicts or synergies) are likely among those services or 

the ecosystem processes that produce them?

What are the threats to various habitats or the species using them?

What actions would enhance or diminish the amount or value of ecosystem 

services? 

•	 Take a broad, long-term perspective. The goals should account for both 

long-term change in the estuary and spatial patterns at all scales. Research 

that informs managers about future conditions and applies broadly across 

the estuary should take the highest priority.

•	 Acknowledge and allow for limitations on gathering knowledge. The 

science goals should be achievable in a reasonable time and realistic 

as to the likely outcomes. Conducting research on subtidal habitats is 

difficult, particularly so in turbid estuaries where these habitats are largely 

invisible. These limitations should be acknowledged in determining 

research priorities and sequencing, and in setting expectations for the 

information needed for restoration and protection.

1. This summary presents the broadest level goals. More detailed, specific objectives and actions can be found 

in the report.
Executive Summary • S-13

SCIENCE GOALS

Soft Substrate 

Understand the extent of ecosystem services provided by soft-bottom habitats.

Understand the threats to mudflats and other soft-bottom habitats.

Determine suitable methods for protecting mudflats and beaches.

Understand the magnitude of the ecological risks posed by contaminants bound to the 

sediments.

Rock Habitats

Understand the ecosystem services provided by rock habitat and the species dependent on 

them.

Understand the ecosystem services provided by restored rock habitat.

Artificial Structures

Understand how artificial structures generally affect the estuarine ecosystem.

Determine the roles of individual artificial structures proposed for removal.

Shellfish Beds

Understand the ecosystem services the shellfish beds support, and in what quantities, in their 

current state and after restoration.

Understand the factors controlling the development and persistence of oyster and other 

shellfish beds.

Develop the most effective ways of restoring and protecting oyster beds.

Submerged Aquatic Vegetation (SAV)

Understand the ecosystem services the eelgrass beds support, and in what quantities, in their 

current state and after restoration.

Understand the factors controlling the development and persistence of eelgrass beds.

Develop the most effective ways of restoring and protecting eelgrass beds.

Assess the status and distribution of other SAV.

Macroalgal Beds

Understand the roles of macroalgal beds of different species in providing ecosystem services 

or interfering with services provided by other habitats.

Understand changes in the extent or condition of macroalgae.
S-14 • San Francisco Bay Subtidal Habitat Goals Report

The Protection Goals

Protection goals for each of the habitat types focus on preserving existing 

habitat. When information about specific threats to each habitat was available, 

more detailed protection objectives and actions were included. 

The resource management committee prioritized stressors that can degrade 

or otherwise influence subtidal habitats, and the administrative core group 

conducted an exercise to compare severity, scope, and irreversibility of these 

stressors against each subtidal habitat type (see Appendix 1-1). This exercise 

resulted in the following key conclusions:

•	 Bottom disturbance is a stressor of concern across several habitats. 

•	 Placement of artificial structures is a potential stressor of concern for the 

shellfish and submerged aquatic vegetation “living” habitats.

•	 Eelgrass habitat has multiple stressors of concern.

•	 Contaminants are a stressor of concern for soft substrate, especially

mud habitat. 

This was the starting framework for developing protection goals. This information was then further developed by science advisor Dr. Wim Kimmerer and 

the science committee (see Appendix 1-1) and incorporated into conceptual 

models for each habitat. Those models more fully describe the functions of and 

threats to the habitats and form the basis for all of the goals for each habitat 

type in Chapters 4–9.
Executive Summary • S-15

PROTECTION GOALS

Soft Substrate 

Consider the potential ecological effects of contaminated sediments when developing, 

planning, designing, and constructing restoration projects or other projects that disturb 

sediments. 

Promote no net increase in disturbance to San Francisco Bay soft bottom habitat. 

Promote no net loss to San Francisco Bay subtidal and intertidal sand habitats.

Develop a coordinated, collaborative approach for regional sediment management for San 

Francisco Bay.

Rock Habitats

Promote no net loss of natural intertidal and subtidal rock habitats in San Francisco Bay.

Artificial Structures

Enhance and protect habitat functions and the historical value of artificial structures in San 

Francisco Bay.

Improve San Francisco Bay subtidal habitats by minimizing placement of artificial structures 

that are detrimental to subtidal habitat function. 

Shellfish Beds

Protect San Francisco Bay native shellfish habitats (particularly native oyster Ostrea lurida) 

through no net loss to existing habitat.

Protect areas in San Francisco Bay with potential for future shellfish expansion, restoration, 

or creation.

Submerged Aquatic Vegetation (SAV)

Protect existing eelgrass habitat in San Francisco Bay through no net loss to existing beds.

Establish eelgrass reserves.

Identify and protect areas in San Francisco Bay for future eelgrass expansion, restoration, or 

creation. 

Protect existing widgeon grass habitat in San Francisco Bay.

Protect existing sago pondweed habitat in San Francisco Bay.

Macroalgal Beds

Protect San Francisco Bay Fucus beds through no net loss to existing beds.

Protect San Francisco Bay Gracilaria beds through no net loss to existing beds.
S-16 • San Francisco Bay Subtidal Habitat Goals Report

The Restoration Goals

In this report, the term “restoration” includes creating, enhancing, remediating, 

and rehabilitating habitat. The restoration goals are not meant to return 

subtidal habitats in San Francisco Bay to conditions that may have existed in 

the past. Rather, they are meant to improve upon conditions that exist today, 

with restoration targets based on what is known about ecosystem services provided by habitats, limiting factors, and the potential for habitats to be created 

or enhanced within the bay. Restoration should also be designed for the 

long term, and planning must therefore account for expected long-term 

changes. Restoration should be targeted to locations and situations where 

long-term success is most likely. This report recommends developing a better 

understanding of the likely success of restoration in particular areas, the local 

processes and conditions as they may affect the habitat, and the present and 

future threats. 

RESTORATION GOALS

Soft Substrate 

Encourage the application of sustainable techniques in sand habitat replenishment or 

restoration projects.

Encourage removal of artificial structures that have negative impacts on soft bottom 

habitat function. 

Rock Habitats

Restore and maintain natural intertidal and subtidal rock habitats in San Francisco Bay.

Artificial Structures

Where feasible, remove artificial structures from San Francisco Bay that have negative or 

minimal beneficial habitat functions.

Promote pilot projects to remove artificial structures and creosote pilings at targeted sites 

in combination with a living shoreline restoration design that will use natural bioengineering 

techniques (such as native oyster reefs, stone sills, and eelgrass plantings) to replace lost 

habitat structure.

Shellfish Beds

Increase native oyster populations in San Francisco Bay within 8,000 acres of potential 

suitable subtidal area over a 50-year time frame through a phased approach conducted within 

a framework of adaptive management.

Submerged Aquatic Vegetation (SAV)

Increase native eelgrass populations in San Francisco Bay within 8,000 acres of suitable 

subtidal/intertidal area over a 50-year time frame using a phased approach under a program 

of adaptive management.

Restoration should be 

targeted to locations and 

situations where long-term 

success is most likely. 
Executive Summary • S-17

Integrating Subtidal Habitat 

Restoration with Other Habitats

Most of the habitat restoration projects implemented in and around San 

Francisco Bay in the last 40 years have focused on single habitat types such as 

marshes and riparian zones. Yet integrating restoration of subtidal and nearby 

marsh and upland habitats may provide greater ecological benefits and cost 

savings, help ameliorate habitat fragmentation, and help protect shorelines 

from climate change impacts, including sea level rise. Integrating subtidal restoration with tidal wetland restoration projects whenever possible thus helps 

protect the enormous investment that has been made over the past several 

decades in tidal wetlands around the bay.

One means to integrate them is through living shorelines. Living shorelines 

utilize a suite of bank stabilization and habitat restoration techniques to reinforce the shoreline, minimize coastal erosion, and maintain coastal processes 

while protecting, restoring, enhancing, and creating natural habitat for fish and 

aquatic plants and wildlife. This technique coined the term because it provides 

Integrating subtidal 

restoration with tidal 

wetland projects helps 

protect the enormous 

investment that has 

been made in restoring 

tidal wetlands around 

the bay.
S-18 • San Francisco Bay Subtidal Habitat Goals Report

“living space” for estuarine and coastal organisms, accomplished by the strategic placement of native vegetation, sand fill, organic materials, and reinforcing 

rock or shell for native plants and animals to settle on.

The decision tree used for vetting goals for the other habitat types (see 

Chapter 2) provides no guidance for integrating subtidal habitats with marshes 

and riparian habitats or for establishing living shorelines. The Subtidal Goals 

Project therefore suggests using an adaptive management approach to implementing pilot restoration projects that integrate subtidal habitat with other 

habitat types.

HABITAT INTEGRATION SCIENCE GOALS

Understand the ecosystem services supported by marsh-subtidal integration and living 

shorelines, and in what quantities.

Develop best practices for integrating subtidal restoration with adjacent wetlands.

Develop best practices for pilot projects to develop living shorelines.

HABITAT INTEGRATION RESTORATION GOALS

Explore the integration of upland, intertidal, and subtidal habitats in San Francisco Bay.

Integrate habitat flexibility to increase resilience in the face of long-term change at habitat 

restoration sites around the bay. 

Explore the use of living shoreline projects as a way to achieve multiple benefits in future 

shoreline restoration.
Executive Summary • S-19

Potential Future Regulatory Actions for Subtidal Habitat 

Several agencies regulate activities within the subtidal area of the bay. Some 

are focused on species protection, fisheries management, or water quality. 

Others have a broader habitat focus, while others must balance ecosystem and 

development needs. In reviewing these goals, some agencies may determine 

it prudent to take regulatory action through their existing authorities or to 

expand their current authorities through legislation or regulation changes. In 

either case, agencies must utilize existing public rule making processes. While 

regulatory measures would likely reduce impacts to the subtidal habitats, more 

research about these habitats is needed. As research is completed to better 

understand the functions and ecosystem services of subtidal habitats, information gained should directly inform management actions. In the interim, the 

Subtidal Goals Project recommends using a precautionary approach in managing subtidal habitats.

Implementing the Goals

To implement the goals, consistent and enduring support will be needed from 

a wide variety of stakeholders and yet may be difficult to secure, given political 

changes, staff turnover, budget fluctuations, and shifts in priorities. Successful 

implementation of the goals will require an entity or entities charged with raising 

funds and overseeing the realization of the goals in this document and the process 

of adaptive management necessary to realize the ecosystem benefits envisioned by 

this program. Implementation will require organizing stakeholders, identifying 
S-20 • San Francisco Bay Subtidal Habitat Goals Report

owners of subtidal parcels, monitoring and tracking restoration projects, 

reviewing and reporting on knowledge gained and on progress in implementing the goals, revising the goals as needed, and educating the public about 

subtidal habitat in the estuary. This implementing entity might be an existing 

organization, a collaborative partnership among several agencies, or a new 

entity (such as a Joint Powers Authority or special district) created for 

this purpose.

The Subtidal Goals Project recommends that the lead entity (or entities) establish a Bay Area Subtidal Habitat Forum (Forum) to engage a broad network of 

agencies and partners who will participate in implementing subtidal habitat 

research, protection, and restoration goals. This Forum, made up of local, state, 

and federal agencies, academic institutions, non-profits, businesses, and industry, would increase regional coordination, collaborative planning, and support 

for and awareness of subtidal protection and restoration. The Forum should 

be charged with leading adaptive management and ensuring progress is being 

made towards the goals in this document. 

Thoughtful planning must be put into the process by which the Forum is constituted, including determining how leadership is selected, which members 

should be included for participation and how they will be selected, what operating practices should be adopted, which agency staff resources will be provided, and what additional funding or resources are needed and where those 

resources will come from. Existing successful regional partnerships such as 

the San Francisco Bay Joint Venture and the Southern California Wetlands 

Recovery Project provide models for such a Forum.

The San Francisco Bay regulatory, agency, and environmental communities have 

an impressive record of taking bold and innovative actions to protect estuarine 

habitats and encourage public involvement. Making the goals set forth in this 

report a reality will take similar bold, sustained, and innovative efforts. The goals 

offer measurable objectives and actions that when implemented, will improve 

San Francisco Bay subtidal habitats. We hope you will join us in embracing 

the principles and recommendations included in this plan and look forward to 

working with a diverse group of stakeholders on implementing the goals.

a note on 

the appendices

Multiple reports informed the 

planning process for the Subtidal 

Goals Project. Because they 

are voluminous, the appendices 

are available on disk inside the 

report’s back cover, and on-line 

at www.sfbaysubtidal.org.
 1

CHAPTER ONE

Purpose of and Need for 

a Subtidal Habitat Goals Report

This san francisco bay subtidal habitat goals report is 

designed to give resource managers, regulatory agencies, environmental 

groups, researchers, industry, and anyone interested in this important 

bay habitat the basic information they need to plan conservation, restoration, 

research, and management activities related to subtidal habitat in the San 

Francisco estuary. 

As defined here, subtidal habitat includes all of the submerged area beneath the 

bay water’s surface: mud, shell, sand, rocks, artificial structures, shellfish beds, 

submerged aquatic vegetation, macroalgal beds, and the water column above 

the bay bottom. 

The Need for a Subtidal Goals Project

In the past several decades, with the goal of improving the San Francisco Bay 

ecosystem, resource agencies and environmental groups have made enormous 

efforts—many are completed or underway, and others still in the planning 

stages—to restore the wetlands at the bay’s edges, the streams and riparian 

areas throughout its watersheds, and, more recently, the remaining open spaces 

of its uplands. Much of this effort has focused on restoring tidal wetlands. 

However, most wetland restoration projects to date have not been designed 

with subtidal resources in mind, despite the fact that subtidal areas are 

intrinsically connected to mudflats, wetlands, creeks, and uplands. Until very 

recently the area beneath the bay’s surface was “out of sight, out of mind”—

unless obstacles needed to be removed or channels dredged to ensure safe 

passage for ships, or when sand, shell, or mud were needed for construction 

and other human activities. 

Government agencies with authority for managing the estuary lack sufficient 

information about subtidal habitats in the bay to inform management 

decisions. Although a tremendous amount of scientific information is available 

from research and monitoring in the bay, little of it is useful in making 

decisions about specific proposals for development or restoration as they relate 

to subtidal habitat. Part of the reason for this shortfall is that subtidal habitats 

Pacific herring (shown here in kelp) 

use eelgrass beds as a spawning 

substrate in San Francisco Bay.
2 • San Francisco Bay Subtidal Habitat Goals Report

are usually invisible in the bay’s turbid waters, and most sampling methods 

cannot provide detailed information about the location and condition of the 

various habitats. Furthermore, relatively little research has been conducted that 

would provide key support for the Subtidal Goals Project on the extent and 

value of the ecosystem services provided by each habitat, and the threats those 

habitats face—information that is needed to protect and restore these habitats. 

Equally important is the need to learn more about the functions of these 

habitats, how they respond to environmental change, and how to protect and 

enhance them. 

A number of ongoing planning efforts successfully address various aspects 

of natural resource conservation in the San Francisco Bay region (see 

box for a list of other such planning efforts). Many of these planning 

efforts address components of subtidal habitats from different planning or 

regulatory perspectives, depending on the entities involved in the efforts 

and their individual mandates and authorities. The Subtidal Goals Project 

is the first effort to focus on all subtidal habitats within San Francisco Bay. 

Implementation of the goals presented here is intended to build upon and 

complement existing efforts. In particular, the perspective of the Subtidal Goals 

Project is physical habitat rather than protection or enhancement of species, 

which is the purview of agencies implementing federal or state Endangered 

Species Acts or regulating collection and harvest.

Other Planning Efforts Related to Subtidal Habitat

Bay Delta Conservation Plan (http://baydeltaconservationplan.com/default.aspx)

Baylands Ecosystem Habitat Goals Project (http://www.sfei.org/)

Comprehensive Conservation and Management Plan (www.sfestuary.org) 

Humboldt Bay Subtidal Goals Project (http://groups.ucanr.org/HumboldtHabitatGoals/)

North Richmond Shoreline: A Community Vision (http://www.restorationdesigngroup.com/

docs/NorthRichmondShorelineVision.pdf) 

Regional Boards Basin Plan (http://www.waterboards.ca.gov/sanfranciscobay/basin_planning.

shtml#2004basinplan)

Regional Monitoring Plan (http://www.sfei.org/rmp/)

Richardson Bay Plan (http://www.tiburonaudubon.org/conserve_planning.html)

Richardson Bay Special Area Plan (http://www.bcdc.ca.gov/laws_plans/plans/plans.shtml) 

San Francisco Bay Plan (http://www.bcdc.ca.gov/laws_plans/plans/sfbay_plan.shtml)

Uplands Habitat Goals Project (http://www.uplandhabitatgoals.org/)

Long Term Management for Disposal of Dredged Material in San Francisco Bay (http://www.

bcdc.ca.gov/dredging/ltms/ltms_program.shtml) 

Dredged Materials Management Office (http://www.spn.usace.army.mil/conops/dmmo.htm)
Chapter One: Purpose of and Need for a Subtidal Habitat Goals Report • 3

Vision Statement

The vision of the Subtidal Goals Project is to achieve, over the next 50 

years, a net improvement of the San Francisco Bay’s subtidal ecosystem 

through science-based protection and restoration of habitats. To achieve this 

improvement, the Subtidal Goals Project proposes: 

•	 Increasing the quantity of desired but currently limited habitats; 

•	 Emphasizing support of native species;

•	 Increasing our understanding of the physical and biological processes 

that affect subtidal habitats and the use of these habitats by species.

Neither a policy nor regulatory document, this report offers guidance on 

opportunities for subtidal restoration and protection. Implementation will 

occur through a number of avenues: local governments may incorporate these 

recommendations into their planning processes and documents, non-profits 

may use them when seeking funding for restoration or management projects, 

and researchers may wish to refer to the report when setting priorities. 

Regulatory agencies may use this report to evaluate, revise, or implement 

their policies. 

New policies or modifications to existing policies proposed on the basis of 

this report will require a separate process in which each agency will analyze 

recommended policies in the context of their existing authorities and public 

input process.

Above and below the surface of the bay (near the Tiburon Peninsula).
4 • San Francisco Bay Subtidal Habitat Goals Report

Planning Framework and Approach

The Subtidal Goals Project is a collaboration among the San Francisco Bay 

Conservation and Development Commission (BCDC), California Ocean 

Protection Council (OPC)/California State Coastal Conservancy (SCC), 

National Oceanic and Atmospheric Administration (NOAA) and the San 

Francisco Estuary Partnership (SFEP). Lead staff from those agencies worked 

with the broader scientific community, managers, restoration practitioners, and 

stakeholders over several years to develop the goals set forth in this document. 

See Appendix 1-1 for details on project methods and participant roles. 

The Goals Project was inspired by the 1999 Baylands Ecosystem Habitat 

Goals report (Figure 1-1), which set a bold vision for restoring 100,000 acres 

of wetlands and related habitats around the bay that have resulted in 13,000 

acres of newly restored habitat, with an additional 40,000 acres acquired and 

in various stages of restoration planning. The Subtidal Goals Project also takes 

a bay-wide approach in setting science-based goals for maintaining a healthy, 

productive, and resilient ecosystem. Where possible, these subtidal goals are 

designed to connect with intertidal habitats and with goals developed by other 

projects, including goals for baylands and uplands habitats. Unlike in the 

Baylands Goals effort, however, historical information about subtidal habitat 

is lacking. Thus the goals set forth in this document do not attempt to restore 

the bay to historic conditions but are designed to improve the condition of 

the subtidal ecosystem. The baseline for the project is 2010, and the planning 

horizon is 50 years.

San Francisco State University 

researchers monitor the eelgrass bed 

at Point Orient on the Richmond 

shoreline.
Chapter One: Purpose of and Need for a Subtidal Habitat Goals Report • 5

Figure 1-1: Map of Subtidal Habitat Goals aligned with Baylands Ecosytem Habitat Goals 

segments (represented by letters), extended to three depth categories: 10', or less, 30' or less, 

and 30' and greater.
6 • San Francisco Bay Subtidal Habitat Goals Report

How the lead agencies will use this report

NOAA, BCDC, SFEP, SCC, and OPC each have different authorities, mandates, 

and policies regarding conservation and management of subtidal habitats. As 

such, each agency may choose to use this document in different ways.

•	 While this document does not supersede or change NOAA authorities or 

mandates, NOAA staff may reference information in this document when 

implementing consultations pursuant to the Endangered Species Act and 

the Essential Fish Habitat provisions of the Magnuson-Steven Fishery 

Conservation and Management Act. 

•	 NOAA may reference this document when evaluating research priorities 

both for NOAA Science Centers and other scientific entities.

•	 The NOAA Restoration Center may use this document to help prioritize 

restoration projects for funding and support.

•	 San Francisco Bay Conservation and Development Commission staff 

may use this document as background material when considering future 

revisions to the San Francisco Bay Plan and may reference this document 

when evaluating proposed projects under BCDC’s existing regulatory 

authority over development in and around San Francisco Bay.

•	 The San Francisco Estuary Partnership may reference information in 

this document when implementing the Comprehensive Conservation 

and Management Plan for San Francisco Bay, in seeking federal dollars 

for San Francisco Bay conservation, and in selecting restoration and/or 

research projects to fund.

•	 The State Coastal Conservancy may use this document to identify 

acquisition opportunities, prioritize conservation and strategic planning, 

and develop restoration projects to support and fund. The Ocean 

Protection Council may utilize the document in making decisions and 

prioritizing research areas, especially as they relate to issues of land-sea 

interface interactions, ecosystem research, and climate change planning.

Background

San Francisco Bay is one of the largest and most important estuaries on the 

West Coast, both for the habitat it provides for fish and wildlife and for the 

many benefits and opportunities it offers people. Its natural beauty gives the 

Bay Area the iconic identity for which it is known throughout the world, while 

its waters ensure an enviable climate and quality of life for over 7.5 million 

residents. The bay provides numerous benefits to humans known as “ecosystem 

services” (see sidebar and Table 1-1). Many residents commute across the 

bay on ferries, or enjoy it while boating, fishing, swimming, windsurfing, 

and birding in and around its waters. Visitors from around the country 

and world are drawn to San Francisco Bay as well: in 2009, the City of San 

Francisco hosted over 15 million visitors, adding some $8 billion to the Bay 

Frequently Used

Terms

Ecosystem: a dynamic 

complex of plant, animal, and 

microorganism communities 

and the nonliving environment, 

interacting as a functional unit. 

A well-defined ecosystem 

has strong interactions 

among its components and 

weak interactions across its 

boundaries.

Habitat: As used by 

ecologists, “habitat” refers 

to a combination of physical, 

chemical, and biological 

conditions that supports a 

population of some species. 

In this document it is used to 

distinguish among areas of the 

estuary mainly on the basis of 

physical configuration, under the 

assumption that suitable physical 

conditions will support desirable 

ecological functions or species.

Intertidal zone: The area that 

is exposed to the air at low tide

and underwater at high tide (for 

example, the area between tide 

marks). This area can include 

many different types of habitats, 

including rocky areas, sandy 

beaches, or wetlands (e.g., vast 

mudflats).

Restoration: Restoration 

is defined as actions taken 

in a converted or degraded 

natural habitat that result 

in the reestablishment of 

ecological processes, functions, 

and biotic/abiotic linkages and 

lead to a persistent, resilient 

system integrated within its 

ecological landscape. For the 

Subtidal Goals Project, the term 

“restoration” is also meant to 

include actions such as creating, 

enhancing, remediating, and 

rehabilitating.

Subtidal habitat: all of the 

submerged area in the estuary.

For more definitions, please see 

the Glossary, Appendix 1-4.
Chapter One: Purpose of and Need for a Subtidal Habitat Goals Report • 7

Table 1-1: Subtidal Habitat Ecosystem Services

Through successful implementation of the subtidal goals and vision, 

the Subtidal Goals Project hopes to sustain and improve upon the 

ecosystem services and functions provided by subtidal habitat.

Soft 

substrate Rock 

Artificial 

substrate

Shellfish 

beds

SAV beds

(submerged 

aquatic 

vegetation 

beds)

Macro–

algal beds

Water 

column

PROVISIONING SERVICES: 

products obtained from the ecosystem such as food (e.g. fishing), fiber, fuel or materials (e.g. sand)

Commercial harvest (i.e., fishing) • • • • • •

Sand and shell mining •

Shipping and ports • •

Marinas • •

REGULATING SERVICES:

benefits obtained through ecosystem processes (e.g., maintenance of air and water quality, erosion control, 

climate regulation, storm protection)

Clean water • • • • •

Shoreline protection • • • • •

CULTURAL SERVICES:

nonmaterial benefits from spiritual enrichment, reflection, recreation, and aesthetic experiences 

(e.g., cultural diversity, educational values, inspiration, sense of place, recreation and ecotourism)

Diversity of ecosystem • • • • • • •

Inspiration for art, folklore, national 

symbols, architecture • • • • • • •

Aesthetics • • • • • •

Sense of place • • • • • •

Recreation—wildlife viewing • • • • • • •

Recreation—harvest • • • • • •

Recreation—boat use •

Recreation—shoreline/beach use • • • •

Ecotourism • • • •

SUPPORTING SERVICES:

indirect services, or those that occur over long periods of time, that are necessary for the production of all other ecosystem 

services (e.g., production of oxygen through photosynthesis, primary production, nutrient cycling, water cycling)

Primary production • • • •

Nutrient cycling • • • • •

Biodiversity • • • • • • •
8 • San Francisco Bay Subtidal Habitat Goals Report

Area economy. The bay is also a busy center of commerce: cargo ships and 

tankers from around the Pacific Rim depend on its ports and infrastructure. 

Approximately two million tons of sand are mined from subtidal areas each 

year for use in construction. Historical oyster shell deposits are mined for 

livestock and chicken feed, soil conditioner, and as a dietary supplement for 

human consumption. 

The bay also supports a variety of “indirect” ecosystem services including 

nutrient cycling, climate regulation, flood protection, water quality 

maintenance, and sediment transport. For more information on these uses and 

benefits of the bay, please refer to Appendix 1-2, the San Francisco Bay Subtidal 

Economic Evaluation Final Report.

In addition to offering these aesthetic, economic, and recreational values, the 

bay supports a critical food web. Herring and Dungeness crab, among many 

other species of fish and shellfish, rear in its waters while sturgeon, salmon, 

and steelhead feed and rest in the bay during their migrations to and from its 

rivers and streams and the ocean. Its vast open water, sloughs, rivers, streams, 

and tidelands host millions of migratory birds every year as they move up and 

down the Pacific Flyway, as well as provide habitat for numerous resident water, 

shore, and song birds. The bay also provides important habitat for marine 

mammals, shellfish, and aquatic invertebrates—the smaller, often unseen but 

important inhabitants of the estuarine ecosystem.

Subtidal habitat is a critical piece of this ecosystem. Although this hidden 

underbelly of the bay is often thought of as a featureless mud bottom, it 

includes a suite of unique habitats: sand waves more than three meters high; 

eelgrass and shellfish beds that act as ecosystem engineers and provide 

substrate for organisms to attach their eggs to and food resources for species 

such as herring and salmon; rocky outcrops covered in seaweeds and 

invertebrates; and mixed sediments in shoals and channel banks that are 

used by a variety of species. Many shellfish, macro- and micro-invertebrates, 

fish, marine mammals, diving ducks, and other wildlife feed, rest, hide, and 

reproduce in these areas. Large populations of shorebirds feed on the estuary’s 

subtidal and intertidal mudflats. 

Above left: Dozens of private and 

public boats join the Queen Mary II 

as it enters San Francisco Bay. Above 

right: Shorebirds forage on intertidal 

and subtidal mudflats.

Herring roe spawn on restored native 

oyster reefs in San Rafael.

Native Olympia oysters attach 

themselves to Pacific oyster shells, 

which are used as a substrate for 

restoration projects.
Chapter One: Purpose of and Need for a Subtidal Habitat Goals Report • 9

The focus of this report is on preserving and restoring the bay’s subtidal 

resources for their ecosystem functions and habitat values and for their 

ecosystem services to humans (see Table 1-1). As such, while all of 

the ecosystem services provided by San Francisco Bay subtidal habitats 

are important, this report identifies a subset of ecosystem services that are 

not directly extractive or destructive of those habitats. The vision statement 

and goals presented herein were developed to support, maintain, and improve 

upon this subset of ecosystem services for continued future benefit to Bay 

Area residents. 

Physical setting

The distribution of habitats within the estuary results from a combination of 

geology, tidal and freshwater flows, currents, wind, biological activity, and 

human activity. The geologic setting of the estuary includes two features that 

are key to its shape and characteristics. First, this tectonically shaped estuary 

bisects the Coast Range, resulting in areas where river flows during lower 

stands of sea level carved out narrow, deep channels (Golden Gate, Raccoon 

and Carquinez Straits) interspersed with broad regions (e.g., South Bay, San 

Pablo Bay) where the estuary spreads into extensive shallow shoals. Second, 

the estuary’s watershed includes 40% of the area of California and some of 

the state’s highest terrain in the Sierra Nevada, providing the fresh water to 

establish a salinity gradient, and sediment that allows shoals to form (and 

keeps the bay turbid). The sediment pulse resulting from hydraulic mining 

in the late 19th century caused over a meter of shoaling in some areas of the 

estuary, and has yet to fully dissipate; when it does, the ensuing sediment 

shortage due to trapping behind dams in the Sierra foothills may cause erosion 

of valued habitats.

The estuary is comprised of the Sacramento-San Joaquin Delta, Suisun Marsh, 

and four basins linked through passes or over shoals (Figure 1-2). All of the 

basins have shallow areas with mud to sand bottom, and deeper channels with 

mainly sand bottom. All have mean depths of 5m or less, except the Central Bay, 

which has an average depth of 12m. Shorelines vary from armored revetments 

to beaches to marsh, and all basins adjoin mainly urban and industrial areas. 

Tidal currents are strong in many parts of the estuary, particularly the narrower 

sections where the estuary penetrates the Coast Range at the Golden Gate and 

Carquinez Strait. Wind is also strong, especially during summer and east of gaps 

in the Coast Range. Wind-driven waves re-suspend sediments and increase 

turbidity locally. Salinity varies from oceanic values near the Golden Gate to 

freshwater values in the northern estuary, typically in Suisun Bay or the western 

delta depending on freshwater flow from the delta.

Suisun Bay is the easternmost of the estuary’s large basins. In the north are 

Grizzly and Honker Bays, which link to Suisun Marsh, a network of channels 

and sloughs adjacent to islands that are mostly managed as freshwater marshes 

for waterfowl, with a small area of remnant natural brackish marshes. A deep 
10 • San Francisco Bay Subtidal Habitat Goals Report

Figure 1-2: Map of sub-basins.
Chapter One: Purpose of and Need for a Subtidal Habitat Goals Report • 11

channel near the southern shore of Suisun Bay links the delta, to the east, to 

Carquinez Strait to the west. A shallower channel to the north connects to 

the main channel near Benicia and Pittsburg. Salinity is typically fresh in wet 

winters and brackish in dry summers and is usually vertically unstratified.

San Pablo Bay is linked to Suisun Bay by Carquinez Strait, a narrow, sinuous 

channel with maximum depth of about 40m. San Pablo Bay has a single deep 

water channel and a broad shoal extending to the northwest. This is the only 

basin with substantial agriculture along the shore. Several salt ponds have 

been restored or are in planning for restoration to tidal wetlands or enhanced 

managed ponds along the northern shore. Brackish tidal marshes adjoin San 

Pablo Bay, including the San Pablo Bay National Wildlife Refuge and the 

National Estuarine Research Reserve site at China Camp. Salinity can be fresh 

during extreme floods but is typically near seawater salinity values in dry 

summers, and is often stratified, especially during high-flow periods. This is an 

important area for migratory shorebirds and ducks.

The Central Bay is the deepest basin, has the largest extent of rocky substrate, 

including areas around islands and seamounts, and is the most influenced by 

the coastal ocean. Much of the bottom is either rocky or sandy, with large sand 

waves illustrating the strength of tidal currents in this region. The deepest 

point is over 100m deep near the Golden Gate Bridge. The water here is the 

saltiest in the bay (on average), with strong stratification present during highflow periods, and is the clearest of all the basins. This region is a crossroads 

for shipping to and from the numerous bay ports, and the most popular for 

water-based recreation such as sailing, because of the dependable winds, varied 

conditions, and spectacular views. Central Bay has the most marine species 

and probably the highest species diversity in the estuary.

New eelgrass shoots from a 

transplant restoration project along 

the San Rafael shoreline.
12 • San Francisco Bay Subtidal Habitat Goals Report

The South Bay is an isolated arm of the estuary. Its shoreline is mostly urban 

and industrial, but in the far south numerous salt ponds adjoin the bay, some of 

them slated for conversion to tidal wetlands or enhanced managed ponds. The 

South Bay Salt Ponds Project is the largest tidal restoration project west of the 

Mississippi. During high-flow periods, salinity in the South Bay is reduced by 

brackish water from the Central Bay and fresh water from streams. During the 

dry season, salinity in the South Bay becomes somewhat elevated because of 

evaporation, and its only freshwater supply comes from wastewater treatment 

plants. The South Bay is also an important area for shorebirds and water birds.

A changed estuary

In addition to historical impacts from gold-mining, humans have altered the 

shape and size of the bay, converted shorelines from marsh to seawall, diverted 

water from upstream rivers, preventing it from flowing into the estuary, added 

innumerable structures to its edges and bottom, removed submerged rocks, 

and plied the bay with ships, boats, trawls, and dredges. 

Activities associated with fishing, marinas, shipping and ports, dredging, sand 

and shell mining, transportation, recreation, and industry have all had impacts 

on the bay’s subtidal habitat. Subtidal habitat is also threatened by invasions of 

non-native species (as a result of human actions, most non-intentional), legacy 

pollutants (such as mercury from gold mining and a variety of chemicals 

formerly used in industry), and modern-day pollution from “point sources,” 

such as industry and sewage treatment plants, as well as “non-point sources,” 

such as the runoff from our streets and watersheds. 

Since the Gold Rush, the bay has lost more than 90% of its historic tidal 

wetlands. Filling of the shoreline and in the bay has shrunk the bay by almost a 

third. This has caused a substantial (but unknown) loss of subtidal habitat. This 

loss and degradation has decreased the value and extent of habitat for many 

species. The biomass of wetland and subtidal vegetation and shellfish has been 

Above: Sand dredger in San Francisco 

Bay. Right: Maintenance dredging at 

the Port of Richmond.
Chapter One: Purpose of and Need for a Subtidal Habitat Goals Report • 13

reduced; these resources likely provided copious food resources to humans 

and animals alike in the past. The intricate matrix of wetland channels, with 

their three-dimensional surfaces, has been filled in to build salt ponds, urban 

landfills, airports, ports, and marinas. The resulting loss of habitat complexity 

probably reduced the abundance of many types of estuarine and marine 

organisms and the productivity of pelagic and benthic food webs. Yet despite 

these changes and challenges,1

 estuarine life persists. 

Report Scope, Content, and Organization

The geographic scope of the Subtidal Goals Project is San Francisco Bay from 

Sherman Island west to the southern extent of the bay and seaward to the 

Golden Gate (Point Bonita to Point Lobos). Although the delta is not included 

in the project scope, conditions in the delta and their relationship to subtidal 

habitat in the bay are addressed in the sections on freshwater input and climate 

change (Chapter 3). For the purposes of this project, “subtidal habitat” includes 

all submerged areas of the bay. 

This report describes six subtidal habitat types with maps showing their known 

current distributions, and analyzes present-day threats to those habitats. 

It presents recommendations for addressing those stressors, for advancing 

scientific research and understanding, and for protecting and restoring subtidal 

habitat within the constraints and challenges of an urbanized estuary and 

incomplete knowledge. It also describes some of the pioneering efforts that 

have taken place to restore subtidal habitat in the bay. Where appropriate, the 

report includes discussion of certain intertidal habitats that are not addressed 

by the Baylands Ecosystem Habitat Goals Project: intertidal mudflats, rocky 

shorelines, sand beaches, and eelgrass and oyster beds.

Chapter 2 describes the considerations used in the planning decisions that 

were made in setting the goals for subtidal habitat. Chapter 3 describes 

both the foundational science goals and other goals that apply to all of the 

habitat types. Descriptions of specific subtidal habitats and the science, 

protection, and restoration goals for each of them are set forth in Chapters 4 

through 9. Chapter 10 focuses on integrating subtidal planning with wetland 

and shoreline planning, while Chapter 11 presents recommendations for 

implementation of the goals. A companion document, NOAA’s August 2007 

Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco 

Bay (http://www.swr.noaa.gov/hcd/HCD_webContent/nocal/SHABTinSFBay.

htm), summarizes existing information regarding subtidal habitats and species 

use in San Francisco Bay. 

1. For a more comprehensive description of human impacts on subtidal habitat since the time of European 

settlement around the bay, see Appendix 1-3.

 15

CHAPTER TWO

Planning Decisions and Considerations

The subtidal goals project focuses on habitats rather 

than individual species (except for those habitats that are created 

by a single species, e.g., eelgrass or oyster beds), an approach that 

avoids prioritizing some species over others. The key decisions and planning 

considerations described here were developed by the administrative core 

group representing the lead agencies, with extensive input from all of the active 

committees and consultants (see Appendix 1-1 for more information about 

committee roles and processes). The following key decisions were made in 

identifying goals for subtidal habitat:

•	 The geographic scope of the Subtidal Goals Project is San Francisco Bay 

from Sherman Island west to the southern extent of the bay and seaward 

to the Golden Gate (Point Bonita to Point Lobos). Although the delta 

is not included in the project scope, conditions in the delta and their 

relationship to subtidal habitat in the bay are addressed in the sections on 

freshwater input and climate change (see Chapter 3).

•	 For the purposes of this project, “subtidal habitat” includes all submerged 

areas of the bay. The project also includes certain intertidal habitats that 

were not specifically addressed in the 1999 Baylands Ecosystem Goals 

Report: intertidal mudflats, eelgrass, sand beaches, rocky intertidal and 

subtidal areas, and artificial substrate.

•	 The report uses a precautionary approach, erring on the side of 

conserving and protecting resources. 

•	 Available information about existing conditions serves as a baseline.

•	 The goals build upon opportunities and information developed by 

existing subtidal pilot projects, including in-the-water monitoring, 

restoration, mitigation, and research projects in San Francisco Bay.

•	 This document avoids setting priorities among habitats; however, 

restoration of some may result in conversion of others. For example, some 

soft substrate may be lost or enhanced through restoration of eelgrass or 

shellfish beds.

•	 Because there is a great deal of uncertainty about the functions and 

value of subtidal habitats and the utility and likely success of restoration, 

The administrative core group held 

multiple meetings with committee 

members and stakeholders to discuss 

Subtidal Goals development.
﻿16 • San Francisco Bay Subtidal Habitat Goals Report

this report recommends using an adaptive management approach in 

implementing the goals. See discussion of adaptive management later in 

this chapter.

•	 As part of adaptive management, progress on achieving the goals—as 

measured by improved scientific understanding and practical experience 

in subtidal habitat restoration and protection—should be reviewed and 

evaluated in a report by 2020. The goals can then be modified as needed. 

Interim updates on particular topics can potentially be provided within 

10 years, and discussed at regional forums and conferences.

Rationale for Setting Goals

Goals for each of the subtidal habitats are based on the Vision Statement 

described in Chapter 1 and the Foundational Science Goals described in 

Chapter 3, taking into account the extent of scientific understanding of 

each habitat. These specific habitat goals lead to actions in one of four broad 

directions: 

•	 Enhancing, creating, or restoring particular habitats

•	 Protecting habitats 

•	 Observing habitats, taking no action

•	 Eliminating artificial habitats

This section describes the process that was used in choosing a course of action 

for investigating, protecting, and restoring each habitat. The process began with 

a determination that a given habitat is likely to provide some valued ecosystem 

services, and then proceeded through a decision tree to determine the most 

suitable course of action (Figure 2-1). 

Eelgrass thrives in Raccoon Strait

between Angel Island and the Tiburon 

Peninsula.
Chapter Two: Planning Decisions and Considerations • 17

The decision tree helped decide which of these ecosystem services to 

emphasize, and how far to go in taking protection or restoration actions 

for a particular habitat. This process is not meant to be static. Improved 

knowledge, including experience gained through progress toward achieving 

the goals, and changes in the system will require revisiting these decisions 

periodically. This can be done through a formal program of adaptive (i.e., 

experimental) management, discussed later in this chapter.

Vetting each habitat through Figure 2-1 led to the following conclusions (more 

specific details are presented in Chapters 4–9): 

•	 Subtidal shoals to intertidal mudflats support valued services and 

are under various threats from human activities and climate change. 

Opportunities for restoration are based on uncertain techniques, so this 

report emphasizes protecting habitat and applying restoration methods 

experimentally.

•	 Muddy soft-bottom habitat is essential for some species and probably 

supports the most ecosystem services of any habitat. Although softbottom habitat is plentiful in the bay, it is threatened by various activities. 

Few opportunities exist to restore it, so protection goals are emphasized 

instead.

•	 Sand bottom is mined for sand, but little is known about its role in 

non-extractive ecosystem services. This lack of knowledge leads to a 

recommendation to protect existing sand resources while learning more 

about the impacts of sand mining and the value of this habitat type to 

species and the ecosystem services it provides. 

•	 Rock outcrops support ecosystem services and are under threat, but 

restoration would be logistically difficult and therefore unlikely, calling 

for protection actions and research-based pilot restoration only.

Goals for 

Restoration

Goals for 

Protection Research No Action

Threats or 

Shortage

Outcomes/Limits 

of Restoration Knowledge

HABITAT X

What does habitat do?

(Ecosystem Services)

3541 g. 2-1 decision tree

Yes No

Feasible Unknown Insufcient Sufcient

Infeasible

Figure 2-1: Decision tree for the Subtidal Habitat Goals Project, illustrating the pathway

considered in the goal development process.

West Coast Native Oyster meetings

bring together researchers and 

restoration practitioners working on 

native oyster projects in California,

Oregon, andWashington.
﻿18 • San Francisco Bay Subtidal Habitat Goals Report

•	 Artificial structures support valued ecosystem services but also can 

impair others. Since they are artificial, most of them cannot be considered 

to be in short supply, nor are they under threat. Conversely, there is 

interest in removing some of them, leading to an expansion of other more 

favorable habitats.

•	 Several habitats (e.g., eelgrass, oyster beds) have clear benefits in 

supporting valued ecosystem services, although the degree of support is 

uncertain. They are likely in short supply and under various threats, and 

restoration has been successful at small scales. Therefore restoration goals 

are the principal focus for these habitats, although protection goals are 

also necessary. 

•	 Macroalgal beds support ecosystem services (although at a small scale), 

but they can also be nuisances under some conditions. Because it is 

unknown whether and which species of macroalgal beds are under threat 

or in short supply, the decision tree process led to identifying research 

goals only.

•	 The water column forms the background for all of the other habitats. It 

supports all ecosystem services. Its existence is not threatened, but water 

quality could become degraded. However, as discussed in Chapter 3, 

water quality is the province of various agencies and is not addressed in 

this project.

Considerations for Research

Three key principles govern the establishment of science goals for subtidal 

habitats:

1. Acknowledge key gaps in the knowledge needed for effective protection 

and restoration;

2. Take a broad, long-term perspective; 

3. Acknowledge and allow for limitations on gathering knowledge. 

Key knowledge gaps: These gaps include such fundamental information as the 

spatial extent of some of the habitats and their functions in the ecosystem. 

Filling these gaps will take time, but that should not delay actions to protect 

habitats. Rather, restoration and protection should be designed and practiced 

to allow for these gaps and to reduce either their size or their effect on 

desired outcomes. In addition, research plans should address the most timecritical knowledge gaps first, specifically in terms of how they will affect 

meeting project goals through protection and restoration activities. These key 

knowledge gaps are set forth below as questions. 

Which ecosystem services do the target habitats support, and how?

This is a relatively straightforward question that can be answered by 

considering the conceptual models of the habitats within the context of the 

Graduate students monitor 

eelgrass beds.
Chapter Two: Planning Decisions and Considerations • 19

overall model. The answer may be “we don’t know,” although we have listed 

ecosystem services likely to be provided by one or more habitats (Chapter 1). 

For example, intertidal mudflats are well known to support various species 

of birds that are either species of concern, have intrinsic value, or provide 

recreational opportunities for birdwatchers. This may be reason enough to 

protect such habitat. By contrast, sandy bottom provides a resource for sand 

mining, but its support of other ecosystem services is poorly understood. 

This points to a key role for research.

What is the relationship between quantity of the habitat and the amount or value 

of those ecosystem services?

This is a much harder question to answer than the previous one, but it should 

form the basis for all decisions about restoration and protection of habitats. 

If the potential area suitable for restoration of a habitat can be estimated, 

what would be the ecosystem-scale response if all of that habitat were to be 

restored? How would that change if only 10% or 50% were restored?

The default assumption is that habitat value increases linearly with habitat 

area, but other responses are possible (Kondolf et al. 2008). For example, 

the number of birds that feed on mudflats in winter could be limited 

initially by feeding conditions in the local habitat and then by conditions 

in their remote summering habitat. In that case, restoration may have little 

effect on birds once the quantity of local habitat exceeded some threshold 

(upper curve, Figure 2-2). Conversely, there may be a threshold of habitat 

area above which some part of the ecosystem shifts into a different, 

preferable state, in which case the cumulative restoration must exceed 

the threshold before this benefit is achieved (lower curve, Figure 2-2). 

What interactions (conflicts or synergies) are likely among those services or the 

ecosystem processes that produce them?

This is one of the more difficult topics, and answers may be limited to 

speculation. In particular, restoration of one habitat implies reduction in 

quantity of another.

What are the threats to various habitats or the species using them? 

Threats are those stressors (Appendix 2-1) that are likely to reduce the 

quantity or impair the quality of a habitat. These include such influences as 

physical damage (e.g., from dredging, sand mining, shipping, trawling, boat 

wakes), contaminants, climate change and sea level rise, and over-harvest. 

Identifying direct threats is fairly straightforward, but indirect threats are 

harder to establish. For example, how would overfishing affect eelgrass beds?

What actions would enhance or diminish the amount or value of ecosystem 

services?

This question is intended to encompass deliberate actions taken either to 

restore a habitat, or to accomplish some other goal (e.g., building a ferry 

terminal) that might affect a habitat. 

3541 fig. 2-2 alt resp Ecosystem Service

Area of Restored Habitat

Early 

Response

Linear Response

Threshold 

Response

Figure 2-2: Schematic diagram of

potential alternative responses 

of the extent or amount of an

ecosystem service to restoration

or loss of habitat area.The benefit

of small-scale restoration depends

heavily on the actual form of this

curve.
﻿20 • San Francisco Bay Subtidal Habitat Goals Report

Broad perspective: The goals should account for both long-term change in 

the estuary and spatial patterns at all scales. Research that informs managers 

about future conditions and applies broadly across the estuary should take 

the highest priority.

The estuarine ecosystem has changed substantially and will continue to change 

(see Table 3-1 and Appendix 2-2). The local influences of climate change that 

have been forecast and observed include rising sea level and a shift to an earlier 

snowmelt peak in the Sierra, resulting in a larger seasonal cycle in freshwater 

flow and salinity. Increasing temperature is likely to have a predominantly 

indirect effect through the northward shift in distributions of organisms, with 

the likely result of species extirpations and species introductions to the estuary. 

Other effects, such as increased wind speed and increased frequency or severity 

of storms, are forecast with less certainty or without consensus among climate 

models. Human responses to climate change, such as building hard structures to 

protect against rising sea level, could have profound effects on subtidal habitats.

Significant impacts from climate change will occur over time scales of decades 

to a century and longer. Over that time frame, many other changes will 

likely occur in the estuary, including population growth, which will result in 

increased demand for water supply, waste discharge, infrastructure, recreation, 

and development near the bay. Changes in transportation such as a substantial 

increase in ferry traffic would have significant impacts on subtidal habits 

throughout the estuary. Changes in management and plumbing of the delta will 

influence annual and interannual patterns of salinity in the bay.

Random or unpredictable events, notably earthquakes but also levee failures 

in the delta, are reasonably sure to happen sometime during the next century. 

Multiple levee failures in the delta will have a tremendous effect on the entire 

estuary because salinity will penetrate farther into the estuary and (in some 

scenarios) the tidal prism will increase. As with sea level rise, human responses 

to these events will affect long-term outcomes; for example, whether flooded 

islands will be diked and drained, and how water managers will respond.

Limits to knowledge: The research goals should be achievable in a reasonable 

time and be realistic as to the likely outcomes. Conducting research in 

natural ecosystems is difficult, particularly so in estuaries. These systems 

are extraordinarily variable in space and time and have myriad interacting 

components, only a handful of which can be observed in a research program. 

Monitoring is essential but generally limited to counts of organisms (e.g., 

fish), collected during the day in deep water. Most ecosystem processes are 

unmonitored. Human impacts are frequent and sometimes subtle, such as 

impacts from contaminants, including oil, and alteration of the sediment 

budget. Finally, the estuary’s water is turbid, and even intertidal habitats 

can be seen only when exposed at low tide. All this is not to say that gaining 

knowledge is impossible, but that these limitations should be acknowledged in 

determining research priorities and sequencing, and in setting expectations for 

the information needed for restoration and protection.
Chapter Two: Planning Decisions and Considerations • 21

Adaptive Management

Adaptive management (Holling 1978, Walters 1986) is specifically designed as 

a way of managing in the face of uncertainty. This approach treats protection 

actions as experiments, acknowledging the value of learning as well as that 

of taking action. This approach is entirely consistent with the current state of 

knowledge regarding subtidal habitats; in most cases, not enough is known 

to support well-informed decisions even about whether to restore or protect 

habitats. In such a preliminary state of knowledge, taking action without an 

experimental, analytical component would be unwise.

Adaptive management (AM) has had a mixed record, mainly because of 

institutional resistance to implementation and because many people use the 

term without fully understanding the meaning. One of the key impediments 

to AM arises in attempts to apply it to large, complex, unreplicated systems. 

When the system can be subdivided to allow for replication and controls, the 

experimental aspects of AM become much more powerful and informative. 

The Subtidal Goals Project is therefore ideally suited to an adaptive approach at 

the project level, because habitats can be subdivided for different treatments. 

Numerous documents outline the approaches to be used in AM (for example, 

Thom 2005). Most center on a diagram of the AM process emphasizing that the 

process is cyclic and has multiple decision points. Figure 2-3 presents such a 

diagram customized for the Subtidal Goals Project. It expands on the decision 

tree in Figure 2-1 to include the key elements of adaptive management. The 

key points to take from this diagram are that AM requires both (1) an explicit 

statement of expectations in the form of models and metrics to evaluate 

progress; and (2) explicit loops from the synthesis of data and re-examination 

of outcomes back to all of the decision points. This process forces managers to 

think about how to measure and display performance and how to determine 

The waters of San Francisco Bay

inside the Golden Gate.
﻿22 • San Francisco Bay Subtidal Habitat Goals Report

Restoration Research

No Action

Threats or 

Shortage

Desired 

Outcomes

What does habitat do?

3541 g. 2-3 adapt mgmt

Yes or Uncertain No

Revise 

Outcomes

“Maintenance” changed to 

“Protection” for consistency 

with Fig. 2-1, OK?

Conceptual/Simulation 

Models

Select Actions

and Metrics

Select Actions

and Metrics

Protection

Monitor and 

Evaluate 

Outcomes

Synthesize and 

Re-examine

Rene 

Models

Rene 

Actions

Reassess Threats, Needs

Figure 2-3: Flow diagram of the sequence of activities in adaptive management in the Subtidal

Habitat Goals Project. Starting from the top, the ecosystem services provided by the habitat are

identified; then threats to the habitat or shortage of the quantity of that habitat are evaluated.

This may lead to a decision to take no action (see Figure 2-1); otherwise, a series of steps are

taken including making decisions about desired outcomes, development of models, and choice

of scale of the action.The action may emphasize restoration, maintenance of the habitat (e.g.,

through regulatory protection), or research. Every one of these actions, however,requires a

set of metrics to evaluate progress, and a process of monitoring and evaluation that leads to

periodic synthesis and re-examination of the action.This results in a feedback loop in which any

of the decision points or preparatory activities can be revised and the whole process refined.

The feedback loops would likely come at progressively longer time scales going up the diagram,

since they would require progressively more complex decisions.

Below: Biologists study invertebrate

use of restored oyster reefs in

San Rafael.
Chapter Two: Planning Decisions and Considerations • 23

whether an action is working as expected. Thus, the key elements of AM that 

distinguish it from most other kinds of management include:

•	 Explicit statements of problems and goals.

•	 Clear conceptual models of processes to be affected.

•	 Predictions of outcomes of the action and potential alternatives, and 

performance measures; predictions may be based on simulation 

modeling.

•	 Designed monitoring programs with embedded analysis for evaluating 

progress toward goals and consistency with the vision.

•	 A team charged with evaluating results and making recommendations for 

revising goals, desired outcomes, models, or actions.

•	 An entity with the authority and will to maintain the process and make 

changes recommended by the evaluation team.

Please see Chapter 11 for additional ideas on how adaptive management can be 

applied to achieve the subtidal goals.

Considerations for Protection

This report is a planning document and not meant to be policy or regulation 

(see discussion in Chapter 1). Agencies and organizations may use this report 

as a guidance document when implementing their authorities and mandates, 

or developing or updating policies. Protection goals included in the following 

chapters were developed with the intent of protecting subtidal habitats in 

San Francisco Bay, and were not weighed against other agency mandates or 

socioeconomic concerns, such as public access or economic development. Any 

policy modification or policy development will entail a separate process in 

which an individual agency will need to analyze the recommendations within 

the context of its existing authorities and mandates. 

This report takes a precautionary approach. When the decision process 

(described above) directed focus on research goals for a particular habitat, 

protection goals were also included in order to maintain existing habitat while 

research is conducted and evaluated for future protection or restoration needs.

Below: Biologists access subtidal

habitats in deep bay muds. Right:A

plankton tow in San Francisco Bay.
﻿24 • San Francisco Bay Subtidal Habitat Goals Report

For all habitat types, protection goals focus on preservation. When information 

existed about specific threats, more detailed protection objectives and actions 

were included. 

The resource management committee identified policy-level stressors that can 

degrade or otherwise influence subtidal habitats:

1. Freshwater inflow

2. Invasive species

3. Climate change

From this list, freshwater inflow and climate change were looked at in a broad 

sense (see Chapter 3), and specific goals were developed for invasive species 

(see Chapter 3). Funding allowed five additional stressors to be evaluated, so 

the resource management committee prioritized five stressors that can degrade 

or otherwise influence subtidal habitats: 

1. Contaminants 

2. Bottom Disturbance

3. Suspended Sediments

4. Placement of Artificial Structures

5. Nutrients

Consultant Dr. Andrew Cohen developed narrative descriptions for each 

stressor (see Appendix 2-1). Working with the resource management 

committee, the administrative core group conducted an exercise to compare 

severity, scope, and irreversibility of these stressors against each subtidal 

habitat type (see Appendix 1-1). This exercise resulted in the following key 

conclusions:

1. Bottom disturbance is a stressor of concern across several habitats. 

2. Placement of artificial structures is a potential stressor of concern for the 

shellfish and submerged aquatic vegetation “living” habitats.

Creosote pilings provide roosting 

areas for birds.
Chapter Two: Planning Decisions and Considerations • 25

3. Eelgrass habitat has multiple stressors of concern.

4. Contaminants are a stressor of concern for soft substrate, especially

mud habitat. 

This was the starting framework for developing protection goals. This 

information was then further developed by science advisor Dr. Wim Kimmerer 

and incorporated into conceptual models for each habitat, which more fully 

describe the functions of and threats to the habitats and form the resulting 

basis for all of the goals (see Chapters 4–9).

Considerations for Restoration

In this report, the term restoration includes creating, enhancing, remediating, 

and rehabilitating habitat (see definition in Chapter 1). The restoration goals 

are not meant to return subtidal habitats in San Francisco Bay to conditions 

that existed in the past. Rather, they are meant to improve upon conditions 

that exist today, with restoration targets based on what is known about limiting 

factors and the potential for habitats to be created or enhanced within the bay.

Restoring a habitat should be undertaken with a clear view of the long-term 

prospects for success whenever possible, using an adaptive management 

approach. This will require answers to the research questions in the following 

sections. Although there are gaps in knowledge, restoration should still be 

pursued at an experimental level based on potential habitat distributions. An 

assessment could begin by determining the maximum possible extent of valued 

habitats for which restoration or protection is an identified priority, such as 

eelgrass and oyster beds and mudflats. How much of that habitat is actually 

likely to exist over the next 50 years, at what level of effort and cost, and what 

will be the result in terms of ecosystem services? (See Foundational Science 

Goal 1 for each habitat type in Chapter 3.) Answers to these questions, however 

approximate, will help to scale expectations and plans for restoration, and these 

answers will be refined as knowledge improves.

Restoration should also be designed for the long term, and planning must 

therefore account for expected long-term changes (see Foundational Science 

A derelict creosote piling structure 

slowly falls into the bay.
﻿26 • San Francisco Bay Subtidal Habitat Goals Report

Goal 2 for each habitat type in Chapter 3). Restoration should be targeted to 

locations and situations where long-term success is most likely. This requires a 

better understanding of the likely success of restoration in particular areas, the 

local processes and conditions as they may affect the habitat, and the present 

and future threats. 

Mapping of Subtidal Habitat

An important first step in developing the subtidal goals was collecting and 

mapping baseline subtidal habitat geospatial data for the entirety of San 

Francisco Bay. The Subtidal Goals Project has assembled existing subtidal 

habitat data layers and created the first set of comprehensive GIS maps1 

illustrating the locations and extent of the bay’s core subtidal habitats.2 See 

also Figure 2-4. Habitat data, from side-scan sonar and multibeam data and 

sediment samples, were compiled from a 2003 report (Greene et al 2003), as 

well as anecdotally from experts involved in the Subtidal Goals Project. The 

2003 report distinguished 91 different bottom types in the Central and South 

Bays at the time of data collection although these likely change as strong tidal 

currents transport sediments around. For the purposes of this project, these 91 

habitat types were consolidated, on the basis of their predominant sediment, 

into 6: soft substrates (including mud, sand, gravel, cobble, and shell mix); 

rock; artificial structures; shellfish beds; submerged aquatic vegetation beds; 

and macroalgal beds. This approach, while necessary for the purposes of the 

project, undoubtedly simplifies habitat types throughout the bay, when in 

reality most subtidal areas are a vast combination of varying and ever-changing 

substrates. 

In addition, existing data layers of activities (and artificial structures) that 

can impact the bay’s subtidal habitats were collected and mapped to spatially 

illustrate the relationship between habitats and stressors. Finally, for some 

habitat types in the bay, proposed restoration sites are shown, based upon areas 

that had successful existing pilot projects or were identified as suitable habitat 

(see Chapters 7 and 8). Three types of maps were created and included in this 

report:

1. Habitat distribution maps

2. Stressor maps. There are four main stressor categories, and each has 

multiple activities that have been mapped:

1. The information for the GIS maps for the San Francisco Bay Subtidal Habitat Goals Project came from a 

variety of sources, including NOAA’s 2003 Electronic Navigation Charts and 2006 Environmental Sensitivity 

Index; 2002 CDFG Bathymetry maps; Gary Greene et al. October 2003 Report: Benthic Habitat Maps of 

San Francisco Bay Interpreted from Multibeam Bathymetric Images and Side-Scan Sonar Mosaics; Merkel 

& Associates, Inc. 2010. San Francisco Bay Eelgrass Inventory October–November 2009. Submitted to: 

California Department of Transportation and National Marine Fisheries Service.; Native oyster survey 

data Grosholz et al. 2007; the Water and Emergency Transit Agency (WETA); the San Francisco Harbor 

Commission; the U.S. Coast Guard; and others. Subtidal Habitat Goals Project committee members 

also provided anecdotal information based upon their knowledge of habitat distributions, which was 

incorporated into the maps. 

2. For a description of additional mapping and surveying needs, see Chapter 11.
Chapter Two: Planning Decisions and Considerations • 27

Figure 2-4: San Francisco Bay Bathymetry Map (NOAA 2010 from CDFG 2004), broken down

into three depth categories: less than 10', less than 30', and greater than 30'.
﻿28 • San Francisco Bay Subtidal Habitat Goals Report

· Activities that increase or redistribute contaminants: wastewater 

discharge, coastal industry (power generation, oil refining, and 

chemical processing), dredging and disposal, sand mining, shell 

mining, commercial fishing, research and education, natural resource 

management and restoration, and urban development.

· Activities that increase bottom disturbance: shipping, construction of 

marinas, ports and wharfs, dredging and disposal, sand mining, shell 

mining, commercial fishing, research and education, natural resource 

management and restoration. 

· Activities that increase suspended sediments: commercial fishing, 

dredging and disposal, sand mining, shell mining, research and 

education, natural resource management and restoration, and urban 

development. 

· Placement of artificial structures: ports and wharfs, pilings, buoys, 

berthing areas, beacons, duck blinds, among others; and activities 

associated with coastal industry, bridges, wastewater discharge, 

commercial shipping and recreational boating, and urban 

development.

3. Proposed restoration site locations: native oysters, native eelgrass, and 

suggested pilot locations for intertidal sand beaches and living shorelines. 

4. Ownership of the subtidal lands: public and private parcel ownership 

data. (See Figure 2-5.)

Although there are some data gaps that need to be filled and more maps 

that need to be made (see next section), the maps in this report should 

allow individuals, agencies, non-profits, governments, and others to see 

the submerged areas of the bay in an entirely new light. With these maps, 

Surf scoters on open water.
Chapter Two: Planning Decisions and Considerations • 29

Figure 2-5: San Francisco Bay Subtidal Lands Parcel Ownership. Parcel

ownership data compiled by Dan Robinson, NOAA fellow at BCDC, 2008.
﻿30 • San Francisco Bay Subtidal Habitat Goals Report

interested parties will be able to access a wealth of data and new information 

for use in their own projects. These maps will

•	 improve existing resource management

•	 provide better data for use in research projects

•	 allow a finer assessment of stressor impacts on particular habitats at given 

site locations

•	 highlight appropriate restoration project sites

•	 facilitate improved cumulative impact assessments

•	 illustrate and help resolve overlapping human use conflicts

•	 allow consideration of lands for acquisition and restoration

The information in the maps can also be used in potential future Marine 

Protected Area or Marine Spatial Planning projects in San Francisco Bay.

Additional Mapping and Data Needed to Implement the Goals

1. Nearshore bathymetry: Updated bathymetry data for the entirety of the 

bay, and specifically for the bay’s shallow areas from the shoreline to 3m 

below mean sea level. Existing bathymetric data sets do not show this area 

accurately enough to properly manage impacts and implement protection 

strategies.

2. Physical setting: Stratigraphy needs to be determined bay-wide to better 

understand the structure of habitats. More than 90% of the bay’s bottom 

is made up of soft, unconsolidated sediments. Research goals in Chapters 

4–9 provide the basis for the need to better define areas of mud, sand, and 

shell hash, so managers can better assess potential impacts and protection 

strategies. Because they have been mapped as navigation hazards, large 

Central Bay segment of historic

hydrographic sheets developed by

the former US Coast Survey.
Chapter Two: Planning Decisions and Considerations • 31

rocky outcrops are probably the best mapped habitats, but small rock and 

cobble could be better delineated in the bay. 

3. Living bottom types: Excellent mapping data are available for native 

oysters in intertidal and shoreline areas. But there is only anecdotal 

information supporting the existence of subtidal populations of native 

oysters, and these areas have never been mapped. Eelgrass beds were 

mapped in 2003 and again in October 2009 by Merkel & Associates, Inc., 

but ongoing monitoring is needed to understand interannual variability 

in distribution and density of all subtidal habitats, particularly for 

macroalgal beds and submerged aquatic vegetation other than eelgrass 

since no spatial data exists for these habitats.

4. Tracking soft-bottom habitat types: High-resolution sub-bottom seismic 

reflection profiling systems can be used to determine the thickness of 

sedimentary units, which, along with repeated bathymetric surveys, can 

then be used to track the dynamic and ever-shifting nature of the bay’s 

subtidal habitats. Using this data, a mapping effort could be undertaken 

to distinguish persistent and temporal habitats and address the dynamic 

influences that re-work the bay-floor. 

5. Hardened shorelines: There is a need to better understand fill type, 

especially in regard to assessing the impact of wave velocities and rising 

sea levels in order to better predict their impacts on foreshore slopes. 

Understanding various fill types and the nature of hardened shorelines 

better informs the planning of subtidal restoration sites and techniques, 

as well as helps plan for sea level rise and other climate change impacts 

throughout San Francisco Bay. 

6. Submerged creosote pilings: The San Francisco Estuary Institute SFEI) 

and NOAA conducted a detailed survey and mapped most of the creosote 

piling complexes that could be seen at low tide above the surface via boat 

(see Appendix 6-1). This survey documented over 33,000 derelict pilings 

in the bay, and estimated at least that many more pilings (and stubs of 

pilings) occur below the surface of the water at low tide. Beyond locating 

and mapping these submerged pilings to improve navigational safety, this 

mapping effort provides information for any potential future removal 

projects.

7. ESI data: NOAA’s Environmental Sensitivity Index maps were released 

in 2006. Since then, innumerable changes have occurred to the bay 

shoreline. The Environmental Sensitivity Index (ESI) Maps for California 

are being updated, pending funding. An update to the San Francisco 

Bay ESI maps is needed to include the most recent information on the 

location and extent of subtidal habitats along the shoreline, any changes 

to management boundary areas, and subtidal restoration projects.

Researchers at the San Rafael

oyster and eelgrass restoration site.
﻿32 • San Francisco Bay Subtidal Habitat Goals Report

8. NOAA’s hydrographic sheets: Based on data collected in the bay since 

the 1850s by the former Coast Survey, NOAA’s “H” sheets are similar to 

the Terrestrial “T” sheets, which have been valuable in developing maps 

to illustrate the comparison between past and present wetland habitats 

in the bay (see SFEI’s Ecoatlas). “H” sheets include depths based on boat 

soundings and information about bottom types based on bottom grab 

samples. Nearly all of the depths on the H sheets have been digitized (Dr. 

Bruce Jaffe, USGS, 2010, pers.comm.), but additional work needs to be 

done to analyze the bottom type against current conditions. 

9. Human uses: Although the Subtidal Goals Project has gathered extensive 

data on human activities that may impact subtidal habitats, additional 

mapping of the bay’s current and predicted future human uses is needed 

to assess stressors and restoration site considerations.

10. Oil spill response: The Office of Oil Spill Prevention and Response GIS 

maps should be regularly updated to include high priority subtidal 

protection areas and locations of available equipment, and used during 

future oil spills in San Francisco Bay.

11. Database and mapping tool for active subtidal restoration and monitoring 

projects: Such a database could be accessed and used by multiple partners 

(academic, non-profit, consultant, and agency). The subtidal database 

could be linked to existing databases such as the San Francisco Bay Joint 

Venture restoration database and the Wetland Tracker.

Raccoon Strait is one of the

naturally deepest areas of the bay.
 33

CHAPTER THREE

Science and Cross-Habitat Goals 

for All Subtidal Habitat Types

This chapter discusses informational needs and issues that cross 

multiple habitat types, including the water column as a unifying habitat 

type. It includes a conceptual description of all subtidal habitats and 

the water column. It lays out foundational science and research goals for all 

subtidal habitat types, and discusses issues that warrant management and 

restoration goals for all habitats—for example, invasive species, oil spills, 

marine debris, and public access and awareness. 

Conceptual Model for All Habitats

The habitat types discussed in this report (Figure 3-1) include habitats defined 

by physical structure (soft-bottom, rock, artificial substrate), habitats created 

partly by organisms (eelgrass beds, shellfish beds, and macroalgal 

beds), and the water column (see next section). All of the habitats 

except the water column are fixed in place, so the water column 

must be considered as part of these habitats as well as a separate 

habitat itself. 

The various subtidal habitats support valued ecosystem services (see 

Chapter 1), although the degree of support, and the relationship of 

quantity of habitat to level of support, are unknown. Conceptual 

models, including text and diagrams, were developed to describe 

the broader subtidal system, and for each of the habitat types. The 

habitat-specific models in subsequent chapters provide information on what each habitat does, both in terms of its function and the 

ecosystem services it supports. They also describe short- and longterm threats—human and other activities that may impair or reduce 

the amount of each habitat.

The Water Column

In setting goals for subtidal habitat, the Subtidal Goals Project used 

the water column—the water covering submerged substrate, including all volume between the substrate and the water surface—as an 

aspect of the conceptual models for all of the other habitats.

Shallow subtidal habitat at the Marin Islands National 

Wildlife Refuge.
﻿34 • San Francisco Bay Subtidal Habitat Goals Report

The estuary’s water column is both the medium for each of the other subtidal 

habitats and a separate habitat in its own right. The water column transports 

material and organisms to and from the other habitats, and many estuarine 

organisms live their lives entirely within the water column. Since water-column 

processes influence other habitats, understanding these processes is essential 

for managing the other habitats.

More scientific research and monitoring have been done on the water column 

than on any other habitat, and the literature is far too extensive to provide a review 

of it here. Some of this material has been synthesized before (Kimmerer 2004). 

The physical forces that affect the water column, how the water responds, and how 

this interaction affects the organisms living in the water are described below.

Physical dynamics

The principal drivers of water motion in the estuary are, in decreasing order 

of importance, tides, freshwater flow, and wind. Tidal oscillations in the 

coastal ocean move water into the estuary at a dominant period of 12.4 hours. 

Tidally-driven currents and longer-period level changes in the ocean, such as 

those from storm surges, are responsible for most of the mixing and transport 

The bay 

 supports 

 recreation, 

 including

 fishing

 and birding.

Eelgrass Beds

Algae Beds

Intertidal Mudflats

Oyster Beds

 Shipping, 

 dredging, and 

 sand mining 

 can damage 

habitats.

 Sea level rise 

 threatens shorelines 

 and many shallow habitats.

Artificial 

structures 

 have both 

 positive and 

 negative 

 effects.

Rock Outcrops

 Desirable habitats (eelgrass, 

oyster beds, intertidal mudflats, 

and rock outcrops) support 

important species and processes.

 The estuary supports 

 economic activities 

 such as sand mining 

 and fishing and is a 

 key port on the 

Pacific Coast. 

Introduced species 

 such as the overbite 

 clam have disrupted 

 the ecosystem.

Tidal currents 

 fluctuate with tidal 

 height and stir

 up the estuary.

 Legacy pollutants and other

 contaminants from urban

 and agricultural runoff are

 in the bay sediment. 

Hg

Se

Hg

Se

Wind waves stir up 

sediment on shoals.

NaCl

Freshwater

flow affects

salinity.

Figure 3-1: Conceptual diagram for subtidal habitats in the San Francisco Estuary.This diagram

displays some of the key concepts involved in subtidal habitats, particularly the processes linking

habitats with each other and the surrounding land, and some of the threats to the habitats.

Similar diagrams in Chapters 4–9 depict details of each of the individual habitat types, including

ecosystem services they provide and threats to them.
Chapter Three: Science and Cross-Habitat Goals for All Subtidal Habitat Types • 35

of materials in the estuary. Freshwater flow in the rivers entering the estuary 

mainly in the delta induces a net seaward flow throughout the estuary that also 

moves materials and some organisms seaward. The relative importance of this 

net flow compared to tidal flow increases going landward into the estuary. 

Typical net flows of freshwater are a few percent of tidal flows at the eastern 

end of Suisun Bay, and much less than that in central San Francisco Bay.

A prominent outcome of the interplay between freshwater flow and tidal currents is the estuarine salinity gradient. This gradient penetrates into the estuary to the western delta during dry periods, and to western Suisun Bay in 

most winters. Doubling freshwater outflow from the delta moves the salinity 

gradient about 8 km seaward with about a two-week lag time. Salinity at any 

point within that gradient decreases correspondingly with increasing flow. 

The salinity gradient is also a density gradient, which tends to oppose the net 

river-derived flow out of the estuary. The situation is different in the South Bay 

where freshwater input comes from wastewater treatment plants most of the 

time, except during high-flow events in the delta when lower-salinity water 

enters the South Bay from the north.

The interaction between net river flow, opposing density gradient, and tidal 

currents also determines the vertical density stratification, by which currents in 

the deeper channels tend to flow toward land (if averaged over the tidal cycle) 

and surface currents tend to flow to sea. The resulting complex pattern of water 

motion has a profound influence on retention of sediments and organisms 

within the estuary. Wind can modify the tidal currents, especially in shallow 

water (< 1m) through breaking wind waves, and very strong wind can limit 

stratification even in deep water.

Sediment movement is even more complex than water movement because sediment particles can settle to the bottom and be resuspended, and the tendency 

to settle depends on grain size. Wind waves in shallow waters are important 

in resuspending sediments, which are then moved mainly by tidal currents. 

Coarser sediments such as sand are most apparent in high-energy environments where finer sediments can’t settle, including beaches (because of the 

action of wind waves), and deep channels (because of tidal currents). The finest 

sediments, generally clay particles (~1 μm in diameter) remain in suspension 

and are largely responsible for the high turbidity of the water throughout the 

estuary. This suspended sediment load may be decreasing as the pulse of sediment from hydraulic mining dissipates, and because dams have cut off the supply of fine sediment to the bay (Schoellhamer 2009).

Water temperature in the San Francisco Estuary has a rather narrow range 

partly because of the modulating effect of the coastal ocean. Seasonal fluctuations are highest in the delta (10–21°C at Antioch) and lowest at the Golden 

Gate (10–16°C).
﻿36 • San Francisco Bay Subtidal Habitat Goals Report

The pelagic food web

Nearly all estuarine organisms are limited to a certain range of salinity through 

a combination of physiological and ecological effects. Pelagic organisms (those 

in the water column) move with the water and therefore are not subject to 

salinity stress the way benthic organisms (those on the bottom) are.

The food webs of the San Francisco Estuary are supported mainly by phytoplankton production, which is usually low because the high suspended sediment concentration limits light penetration, and in some areas grazing by 

clams limits the buildup of phytoplankton biomass. High ammonium concentrations mostly from wastewater treatment plants in the delta may further suppress phytoplankton growth and production (Dugdale et al. 2007).

This low productivity is reflected throughout the food web. For example, zooplankton throughout the estuary feed mainly on microzooplankton, presumably because phytoplankton biomass is low, and zooplankton are food limited 

much of the time. The low productivity is the principal reason why there is no 

major commercial fishery in the estuary. Another consequence of high turbidity and low phytoplankton productivity is that nutrient concentrations remain 

high most of the time, and eutrophication has not occurred since sewage treatment plants were upgraded in the 1970s. If the trend toward increasing water 

clarity (Schoellhamer 2009) continues, eutrophication might become possible 

sometime in the future.

Interactions

The water-column habitat interacts with all of the other habitats in the bay, and 

with the delta and coastal ocean. Water supplies nutrients, food, and oxygen 

to benthic habitats, removes waste, and redistributes plankton and larvae. Its 

interaction with the soft bottom is particularly important, because of the soft 

bottom’s great extent and because many benthic organisms feed on particles in 

the water column, and in turn are fed upon by fish, crabs, and shrimp.

Exchange with the coastal ocean removes sediment, organisms, and wastes 

from the bay, and brings in coastal organisms. Perhaps more important is 

exchange that occurs through movement of fish and other organisms: there 

is no barrier between the bay and the coastal ocean. Ocean conditions (for 

Volunteers move bags of Pacific

oyster shell by kayak for placement

at the San Rafael restoration site.

Harbor seals haul out on rocks near

the Richmond-San Rafael Bridge.
Chapter Three: Science and Cross-Habitat Goals for All Subtidal Habitat Types • 37

example, El Niño, Pacific Decadal Oscillation) can influence the bay directly 

(through temperature or water level) and indirectly through changes in the 

species composition and abundance of fish that then enter the bay.

Another important exchange is with the rivers entering the delta, which supply 

sediments, nutrients, and organic matter to the water column, but also many 

contaminants such as pesticides, herbicides, mercury, and selenium. Additional 

sources of contaminants are the urban and industrial areas surrounding the 

estuary, ships within the estuary, and contaminants stored in sediments.

The water column is also subject to a variety of human influences that can then 

affect other habitats. These include the various influences of climate and other 

long-term changes (Table 3-1, Figure 3-2, and Appendix 2-2). 

Table 3-1: Long-term changes projected or likely to occur in the estuary, and some potential consequences

for the more seaward reaches of the estuary. Causes in bold are those with a high probability of occurrence,

or that are already observed. Other causes are either weakly or inconsistently supported by models.

Cause Consequence

Sea level rise Habitats will be in deeper water, less suitable because of turbidity; landward shift 

limited by shoreline conditions.

Higher tide and tidal range may increase erosion and alter shorelines, mudflats, 

and marsh boundaries.

Increase in tidal range may increase intertidal area; depends on sediment 

characteristics and sediment supply rate.

Increased salt penetration due to enhanced estuarine circulation.

Increase in tidal range will increase the strength of tidal currents, possible erosion.

Temperature rise Change in phenology, biogeography of estuarine and marine species.

Species introductions and local extinctions.

Reduce survival, reproduction, and growth of eelgrass and native oysters.

Higher winter, lower spring/summer flow (salinity opposite).

Total precipitation More total flow and lower salinity with increase.

Wind speed Increased resuspension of sediment from intertidal and shallow subtidal areas 

with increased wind speed.

Storm frequency Increased shoreline erosion with increased storm frequency.

Acidification Impaired calcification of shellfish. Note that scientific support for ocean acidification 

is very high, but the estuary may respond more to local conditions.

Interactions Higher sea level with stronger currents and wind, accelerate erosion.

Levee failures in delta In short term, rapid rise in salinity (if during wet season); in long term, chronically 

higher salinity.

Changed delta configuration Depending on operating criteria, potential increase in salinity.

Population growth Increased demand for all ecosystem services; increased urbanization, impacts from 

transportation and infrastructure. 

Continued reduction in sediments Continued shortage of sediments to build marshes, mudflats, erosion of shorelines.

Introduced species Impossible to predict; depends on which species and where.

Industrial development Desalination plants may be constructed, with attendant impacts on water column 

and other habitats. Tidal or wave-driven power sources would alter flows and 

increase artificial structures, and possibly have impacts on fish and marine mammals.
﻿38 • San Francisco Bay Subtidal Habitat Goals Report

Figure 3-2. Shoreline areas vulnerable to sea level rise, San Francisco Bay Area.
Chapter Three: Science and Cross-Habitat Goals for All Subtidal Habitat Types • 39

A particular human influence on the water column occurs over long distances: 

alien organisms are introduced through vectors such as shipping, deliberate 

introductions for fisheries (including oysters and their associated fauna), sales 

of live bait, and careless or deliberate introduction of unwanted aquarium or 

food organisms. Although most of the introduced species in South Bay to San 

Pablo Bay have been benthic, the zooplankton species of the brackish regions 

of the estuary are largely introduced, as are the fishes of the freshwater regions. 

The most notable introduction of the last several decades in terms of systemwide impact was that of the overbite clam, Corbula amurensis, whose filterfeeding reduced phytoplankton production of the northern estuary to about 

20% of its previous value.

Protection of the Water Column

This document does not recommend specific goals for water-column habitat. The benthic habitats (e.g., eelgrass) are assumed to include the overlying 

water column for the purposes of setting and achieving goals for those habitats. For example, the movement of propagules (eelgrass seeds, oyster larvae) 

among beds is mediated by water motion, and therefore this motion must be 

considered in efforts to restore or enhance the beds. The greatest concerns for 

protecting the water column are reducing contaminants and improving water 

quality for fish. The effects of emerging contaminants1

 (hormones, antibiotics, 

and other pharmaceuticals) on bay resources have been identified as an area 

of concern and initial protection recommendations are identified (see Chapter 

4). Many of these pollutants are entering the bay through wastewater treatment plants that currently lack the technology to remove them. These issues 

are under the purview of existing agencies operating under various laws and 

authorities, such as the federal Clean Water Act and the Porter-Cologne Water 

Quality Control Act. Recommendations on these topics in this document 

would likely be redundant with existing laws and policies, and were not considered a high priority for this report. 

1. For more information on current science and considerations for the management of Emerging Contaminants, see http://www.calost.org/CA%20CEC%20Workshop%20Final%20Report%20Sept%202009.pdf. 

Corbula clam

The taller invasive

cordgrass on the right

has invaded marshes

throughout the bay.
﻿40 • San Francisco Bay Subtidal Habitat Goals Report

Foundational Science Goals

Scientific uncertainty about subtidal habitats precludes immediate decisions 

about undertaking restoration activities or implementing protective measures. The functions of the habitats, the ecosystem services they support, the 

threats to them, and the prospects for restoration or protection are all poorly 

understood. The goals and questions below form the basis of the science that is 

needed for all of the habitats.

Foundational Science Goal 1

Understand the value of the habitats. 

Question A. What ecosystem services do the habitats support?

Question B. What is the relationship between the extent of desired habitats 

(especially oyster beds, eelgrass beds, and intertidal mudflats) and the extent of 

ecosystem services provided? 

Foundational Science Goal 2

Understand the interactions among habitats.

Question A. How do the various habitats interact, and is there synergy or antagonism between them?

If one habitat provides some benefit (e.g., chemical or biological output, or refuge) to another nearby habitat, the result may be a greater level of ecosystem 

services than would be expected from the individual habitats. 

An obvious interaction occurs in that each habitat can grow only at the expense 

of other habitats. For some habitats this probably doesn’t matter. For example, 

establishing eelgrass beds in all of the feasible locations would make only a 

small dent in the availability of mud-bottom habitat. Because eelgrass will grow 

only in the margins of the bay in suitable substrate, depth, and salinity, it is 

unlikely that the scale of eelgrass restoration would significantly decrease the 

ecosystem services of the soft subtidal substrate. In addition, multiple habitat 

types can coexist in the same area, such as eelgrass blades growing over a soft 

mud bottom. 

Question B. How will these interactions change as the estuary changes?

Long-term changes, particularly sea level rise and decreased sediment supply, 

will alter the way the various habitats function and interact (Appendix 2-2). 

These changes may either amplify or negate the benefits of various actions 

taken in the near term. One possible outcome is a landward movement of the 

shoreline, such that the landforms are similar, and functions continue, but at 

locations farther inland. This can happen only where hardened structures such 

as roads do not impede this landward movement. Therefore understanding this 

future trajectory will be essential in planning actions for all habitats.

Windsurfers on the bay.
Chapter Three: Science and Cross-Habitat Goals for All Subtidal Habitat Types • 41

Foundational Science Goal 3

Understand the long-term prospects for subtidal habitats.

The future trajectory of the estuary is likely to impinge on some habitats, some 

favorably and others not. In addition, long-term changes such as sea level rise 

may increase motivation for restoring certain habitats as part of a strategy 

for adapting to a rising sea. Of all the trends projected, those of sea level rise, 

decreased sediment supply, increasing temperature, increasing salinity, and further species introductions seem to be the greatest threats to subtidal and intertidal habitats. Potential effects of ocean acidification may affect the central bay 

but are likely to be controlled within most of the estuary by local processes.

Question A. What is the current extent of each of the habitat types, and how 

is it changing?

Because subtidal habitats sometimes shift with changing conditions, asking and 

answering this question periodically should be part of any plan for managing 

these habitats. Knowledge of habitat extent is essential to determine and document how the habitats are changing over time and whether restoration goals 

are being achieved.

Question B. How will individual habitats respond to forecasted changes in 

the estuary? 

This question may never be answered, but consideration of these issues should 

provide the underpinning for all decisions about restoration and protection of 

habitat. Although many people are now aware of some of the consequences of 

climate change, relatively few have imagined the state of the estuary 50 years 

hence. The impacts of climate change are numerous, but the impacts of some 

more immediate anthropogenic influences are just as important (Table 3-1); 

although many of these impacts (for example, due to water shortages or levee 

failures) will be most severe in the delta, most will be felt throughout 

the estuary. 

Question C. How is the balance between sediment deposition and erosion likely to 

change, and how will these changes affect subtidal habitats?

The sediment budget of the estuary may now be negative, i.e., there may be 

more erosion than can be supported by the supply of sediment from rivers 

(Chapter 4). This has strong implications for all subtidal habitats, but particularly for soft-bottom and eelgrass habitats.

Question D. What are the likely effects of projected changes in temperature and 

salinity on key estuarine species?

Salinity will likely be closer to oceanic values for more of the year than is currently the case. Pacific herring may require depressed salinity for some part of 

the life cycle. Subtle changes in the food web may alter foraging opportunities 

for fish, birds, and marine mammals.

Biologists survey a new native

oyster restoration site at Cesar

Chavez Park near the Berkeley

Marina.
﻿42 • San Francisco Bay Subtidal Habitat Goals Report

Question E. What are likely effects of the potential loss of 

important transient species such as Chinook salmon?

Higher temperature will have a substantial effect on 

salmon through its effect on survival of spawning 

adults, embryos, and juveniles in the rivers. Loss of 

a substantial fraction of the salmon could remove a 

fairly significant proportion of the fish present in some 

seasons.

Question F. What potentially damaging invaders to the 

estuary might arrive either through range expansions 

due to temperature and salinity changes, or through 

ongoing introductions in ballast water and other vectors?

Question G. How will changing sea level and shoreline 

erosion affect seal rookeries and haulout sites and habitat 

for shorebirds and waterfowl within the bay?

The potential loss of shallow subtidal and intertidal 

areas could drastically alter the availability of what is 

essentially temporary terrestrial habitat for aquatic 

vertebrates and shorebirds. This should be examined 

together with the availability of alternative habitat.

Foundational Science Goal 4

Develop mechanisms to adapt to climate change.

Adaptation to some of the trends identified in Appendix 2-2 may be possible.

Question A. How can restoration and protection measures be established so as to 

accommodate forecasted changes?

Some habitats may be too vulnerable to survive the anticipated changes in all 

locations. Planning for restoration or construction of habitats such as eelgrass 

beds should consider the likely future configurations of various parts of the 

estuary.

Question B. What technologies are available, and how effective are they in adapting to the effects of elevated sea level and loss of sediment supply while protecting 

habitats?

There may be opportunities to adapt to sea level rise and long-term reductions 

in sediment supply through construction practices that provide some habitat, 

through the use of living materials such as eelgrass or oyster beds to buffer and 

protect vulnerable areas from erosion and inundation (“living shorelines”), 

and by linking subtidal restoration with marshes (see Chapter 10). These practices are largely untested and should be attempted only in an experimental 

framework.

Researchers study eelgrass

beds in Richardson Bay.

A researcher shows the length of

San Francisco Bay eelgrass, which

can grow to 2 meters or more.
Chapter Three: Science and Cross-Habitat Goals for All Subtidal Habitat Types • 43

Cross-Habitat Goals

The goals presented in the following sections relate to issues that affect all subtidal habitat types, specifically invasive species, oil spills, marine debris, and 

public access and awareness.

Invasive Species

An “invasive species” is defined as a species 1) that is non-native and 2) whose 

introduction causes or is likely to cause economic or environmental harm or 

harm to human health. Over 230 non-native species now live in San Francisco 

Bay, many of which have altered benthic habitats and water column function by 

modifying the community structure or the physical or chemical environment. 

Invasive species have been introduced in a variety of ways, some intentional 

and some unintentional. Eradication of invasive species is feasible only in 

unusual circumstances, notably during early stages of invasion with an intertidal species that is easy to see and identify. Critical factors to assess before 

committing resources to control or eradication include considering the likely 

harm if the introduced species is left unchecked; whether ecosystem services 

from specific habitats will be reduced; the potential for eradication or reduction to acceptable levels within a reasonable time frame (for example, no longer 

than 10 years); whether the proposed methods for treatment are known to 

work; and whether there is reasonable assurance that no identifiable vector will 

re-introduce the species proposed for control or eradication.

The non-native cordgrasses Spartina alterniflora, densiflora, angelica, and patens were planted in San Francisco Bay for restoration purposes. The plants have 

since become invasive, and S. alterniflora and its hybrids threaten to replace 

pickleweed and native S. foliosa in existing and restored intertidal habitats and 

to overgrow mudflats. The result would be a monoculture of invasive Spartina,

and a major loss of functions and values of these habitats. Since 1999, the California Coastal Conservancy has managed a regionally coordinated effort to 

solve this problem through its Invasive Spartina Project. Over $14 million has 

been spent on Spartina eradication to date.

In 2006, the NOAA Restoration Center and other partners coordinated a successful early eradication effort to control the introduction of the brown alga 

Ascophyllum nodosum at sites in San Leandro Bay. In 2009, the Smithsonian 

Environmental Research Center and other partners began coordinating an 

early eradication effort for known small populations of the introduced alga 

Undaria pinnatifida at two marinas in San Francisco Bay. 

Many invasives move as unknown stowaways and “hitchhikers” when people 

and their products are transported. A wide variety of invasive species have 

found their way into San Francisco Bay in ballast water, holding tanks, and bait 

and seafood packing material, and via fouled vessels. The overbite clam Corbula amurensis is one of the most notable subtidal invasives brought to the bay 

Invasive cordgrass eradication.

Invasive cordgrass is eradicated by

a helicopter spraying herbicide near

Old Alameda Creek at Eden Landing

Ecological Reserve.
﻿44 • San Francisco Bay Subtidal Habitat Goals Report

most likely in ship ballast. Unfortunately, the widespread distribution of the 

species throughout soft-bottom habitats, especially in the northern parts of 

the bay, makes eradication infeasible.

While ballast water moves a much greater number of species, aquaculture is 

probably a far more effective mechanism for introducing exotic parasites, diseases, and other pests of fish and shellfish. For example, Pacific Coast oyster 

growers began importing and culturing Virginia oysters (Crassostrea virginica)

from the Atlantic Coast in 1869, and Pacific oysters (Crassostrea gigas) from 

Japan in 1902, which resulted in many Atlantic and Japanese species (including several oyster pests such as the oyster drill) becoming established in the 

bay. More recent types of marine aquaculture (such as salmon and abalone 

farming) have also released exotic species into Pacific waters (Cohen 2005).

Invasive species control goals focus on removing four invasive species for 

which removal efforts are already underway and eradication is reasonably 

attainable, and on preventing additional invasions. The goals presented below 

represent regional implementation of the California Aquatic Invasive Species 

Management Plan (http://www.dfg.ca.gov/invasives/plan/) as related to subtidal habitats within San Francisco Bay. 

Cross-Habitat Invasive Species Control Goal 1

Minimize the impacts of aquatic invasive species on native 

subtidal habitats in San Francisco Bay. 

•	 Cross-Habitat Invasive Species Control Objective 1-1: Eradicate four 

species of existing aquatic invasive species in San Francisco Bay that affect 

intertidal and subtidal habitats.

Cross-Habitat Invasive Species Control Action 1-1-1: Continue to fund and 

implement the California Coastal Conservancy’s Invasive Spartina Project 

and eradicate Spartina alterniflora (cordgrass) and its hybrids by 2012.

Cross-Habitat Invasive Species Control Action 1-1-2: Identify and secure 

funding for efforts to remove 100% of all Undaria pinnatifida (wakame) 

from San Francisco Bay by 2012.

Cross-Habitat Invasive Species Control Action 1-1-3: Identify and secure 

funding for removal of 100% of all Ascophyllum nodosum (knotted wrack 

weed) material from San Francisco Bay by 2012.

Cross-Habitat Invasive Species Control Action 1-1-4: Continue to support 

funding for exotic oyster and oyster drill removal projects and eradicate 

all known populations of Crassostrea gigas/virginica by 2011.

•	 Cross-Habitat Invasive Species Control Objective 1-2: Prevent 

the introduction or establishment of aquatic invasive species in San 

Francisco Bay. Invasive Undaria pinnatifida beneath 

a dock at the San Francisco Marina.
Chapter Three: Science and Cross-Habitat Goals for All Subtidal Habitat Types • 45

Cross-Habitat Invasive Species Control Action 1-2-1: Establish an expert panel 

to review new non-native species invasions and their potential ecological 

effects when they occur, and make decisions regarding feasibility of 

eradication and reasonable levels of resources.

Cross-Habitat Invasive Species Control Action 1-2-2: Develop and implement 

an early detection monitoring program for high priority aquatic invasive 

species (including but not limited to Zostera japonica, Caulerpa taxifolia or 

other Caulerpa spp., Undaria pinnatifida, Ascophyllum nodosum, Crassostrea 

gigas and C. virginica) specific to the bay. Components would include risk 

assessments to identify avenues for vector introduction, and prioritization of 

ecologically sensitive sites and high concentration areas.

Cross-Habitat Invasive Species Control Action 1-2-3: Develop and implement a 

coordinated system for rapid response, such as the Bay Area Early Detection 

Network, to contain newly detected aquatic invasive species. Identify lead 

agencies that can provide financial and logistical support for rapid response, 

and identify key scientific organizations and agency personnel to lead 

eradication efforts.

Cross-Habitat Invasive Species Control Action 1-2-4: Support improvements 

in ballast water and sea chest inspections through additional training 

and staffing.

Cross-Habitat Invasive Species Control Action 1-2-5: Create an education 

program focusing on proper disposal of non-native algal packing material 

and encourage fishermen to dispose of non-native algal packing material in 

trash receptacles.

Cross-Habitat Invasive Species Control Action 1-2-6: Fund and implement 

clean boating and recreational education programs. Work with the bait 

fish, restaurant, and aquarium communities to develop best management 

practices. Provide outreach materials and signage at marinas, recreational 

shops, and boating facilities to inform users of the risks of accidental release 

of invasive species.

Cross-Habitat Invasive Species Control Action 1-2-7: Use only native species 

in restoration, inspecting all live restoration and construction materials 

for aquatic invasive species and cleaning all equipment prior to and post 

restoration/construction.

Oil Spills 

In the past 15 years, San Francisco Bay and surrounding coastal waters have 

been impacted by several oil spills. Two of the largest spills, the Cape Mohican (40,000 gallons in 1996) and the Cosco Busan (54,000 gallons in 2007) 

impacted miles of bay and coastal habitat. Rocky intertidal, sand beaches, 

mudflats, fringing marshes, and eelgrass beds as well as the animals that 

use them were harmed by these spills. Although large oil spills are relatively 

Invasive Undaria pinnatifida.
﻿46 • San Francisco Bay Subtidal Habitat Goals Report

infrequent, the risk of one happening is always present. Non-point source pollution, including petroleum in runoff from roadways, contributes significantly 

to effects on intertidal and subtidal biota on a more consistent basis.

Types of oil spilled in the bay include crude oil, refined petroleum products 

(such as gasoline or diesel fuel) and by-products, bunker fuel, oily refuse, or 

oil mixed in waste. Spills can take months and even years to clean up. In many 

cases oil washes onto both subtidal and intertidal habitats. Intertidal and 

subtidal shorelines, more than any other part of the marine environment, are 

exposed to the effects of oil, as this is where it naturally tends to accumulate. 

Oil floating on top of water limits the photosynthesis of marine plants and 

phytoplankton, and oil attached to leaves of aquatic vegetation can smother the 

plants. Epiphytes and epibenthic macroinvertebrates can also be smothered in 

the process or can absorb the chemicals.

In some circumstances, subtle changes to rocky shore communities can be 

triggered by a spill, which can be detected for 10 or more years afterwards. 

Soft sediment shores are extremely vulnerable to impacts from oil spills. If 

oil penetrates into fine sediments it can persist for many years, increasing the 

likelihood of longer-term effects. The upper fringe of “soft” shores is often 

dominated by salt marshes, which are generally only temporarily harmed by a 

single oiling. However, damage lasting many years can be inflicted by repeated 

oil spills or by aggressive cleanup activity, such as trampling or removal of oiled 

substrate. 

Immediate oil spill response and cleanup are crucial in minimizing impacts 

to intertidal and subtidal habitats. The Incident Command framework used 

for oil spill response in California is mandated at the state and federal levels. 

The United States Coast Guard, the California Department of Fish and Game 

(through the Office of Oil Spill Prevention and Response), the National Oceanic and Atmospheric Administration, and other trustee agencies are charged 

with working with the Responsible Party (ship owners) to implement response 

and cleanup. The Marine Safety Branch of the Office of Oil Spill Prevention 

and Response is charged with oil spill prevention, and has programs in place 

to monitor on-water fuel transfers, track tug escorts, and work with local 

Harbor Safety Committees to prevent vessel collisions that result in oil spills. 

Because San Francisco Bay has several busy ports and refineries and tanker 

traffic, future oil spills are possible, so continuing to learn from past spills and 

developing spill readiness plans is important. The following goals focus on preventing oil spills from occurring and improving response in order to minimize 

their impacts when they do occur2

.

They include specific recommendations for improving specific subtidal habitat 

protection and response via existing programs and regional coordination and 

response to oil spills. Sewage and wastewater treatments spills also occur in 

2. For more information on the lessons learned from the 2007 Cosco Busan spill, and new legislation in place, 

see http://www.uscg.mil/foia/CoscoBuscan/CoscoBusanISPRFinalx.pdf. 
Chapter Three: Science and Cross-Habitat Goals for All Subtidal Habitat Types • 47

San Francisco Bay, but recommendations in these areas are not included in this 

report (see discussion on water column at the beginning of this chapter).3

Cross-Habitat Oil Spills Prevention Goal 1

Protect San Francisco Bay from both acute and chronic 

oil spills.

•	 Cross-Habitat Oil Spills Prevention Objective 1-1: Enhance oil spill 

preparedness and response capabilities to reduce impacts to subtidal habitats.

Cross-Habitat Oil Spills Prevention Action 1-1-1: Increase coordination with 

Regional Response Teams and develop well-trained teams (including 

Incident Command agencies, local agencies and municipalities, non-profit 

groups, volunteers or others) to assist in rapid response, wildlife recovery, 

and injury documentation. 

Cross-Habitat Oil Spills Prevention Action 1-1-2: Integrate best available 

intertidal and subtidal habitat information into the San Francisco Bay and 

Delta Area Contingency Plan and provide it to all levels of government to 

enhance rapid response booming and subsurface capabilities to protect 

sensitive pelagic and benthic areas. 

Cross-Habitat Oil Spills Prevention Action 1-1-3: On an annual basis, update 

the Office of Oil Spill Prevention and Response’s Environmental Sensitivity 

Index maps and GIS maps to include the most current information on 

locations of sensitive or valued existing or restored subtidal habitats. 

Cross-Habitat Oil Spills Prevention Action 1-1-4: Support the development of 

new technologies (e.g. boom type and size sufficient for San Francisco Bay 

waves and currents and technologies to protect subsurface habitats) for oil 

spill prevention and response specific to the protection of subtidal habitats. 

•	 Cross-Habitat Oil Spills Prevention Objective 1-2: Prevent oil spills 

from a variety of sources, including vessels, pipelines, facilities, vehicles, and 

railroads.

Cross-Habitat Oil Spills Prevention Action1-2-1: Update and improve spill 

prevention technology/programs on pipelines (fueling platforms, wharfs, 

and transfer facilities) and refineries that are located near water. 

Cross-Habitat Oil Spills Prevention Action 1-2-2: Educate boaters and fishermen 

on oil and fuel spill prevention and clean boating practices (e.g., oil 

absorbing bilge pads, used oil recycling).

Cross-Habitat Oil Spills Prevention Action 1-2-3: Support education programs 

that promote automobile oil recycling and vehicle maintenance programs.

3. For more information on regional efforts to reduce sewage and wastewater treatment spills, including 

recent legislation, see http://baykeeper.org/our-work/sick-sewage-campaign.

A US Fish andWildlife Service

biologist monitors a section of

shoreline after the Cosco Busan

oil spill.
﻿48 • San Francisco Bay Subtidal Habitat Goals Report

•	 Cross-Habitat Oil Spills Prevention Objective 1-3: Use Natural 

Resource Damage Assessments (NRDA) to ensure the public is adequately 

compensated for the loss of ecological services to the subtidal ecosystem. 

Cross-Habitat Oil Spills Prevention Action 1-3-1: Develop a centralized 

NRDA database and mapping application, to help responders determine 

spill trajectories and initial priorities after a spill. Use most current 

Environmental Sensitivity Maps and available subtidal data to better 

integrate information on seasonal distributions and habitat use by species 

listed under the Endangered Species Act, other aquatic native species, as well 

as sea and shore birds. 

Cross-Habitat Oil Spills Prevention Action 1-3-2: Coordinate all shoreline 

response and cleanup activities with local resource biologists to prevent 

damage to subtidal habitats. Ensure the Office of Oil Spill Prevention and 

Response’s best practices are implemented by local agencies and private 

landowners (avoid washing rocky intertidal habitats with high-pressure hot 

water, removing un-oiled shoreline wrack, and using dispersants).

Cross-Habitat Oil Spills Prevention Action 1-3-3: Perform baseline monitoring 

and laboratory analysis on the effects of polycyclic aromatic hydrocarbons 

on subtidal habitats and organisms and develop recovery curves (timelines 

for recovery of species and habitats) for use in restoration planning.

Cross-Habitat Oil Spills Prevention Action 1-3-4: Create and maintain a subtidal 

restoration project list and cost estimates for settlement of damages to the 

restored habitats. 

Cross-Habitat Oil Spills Prevention Action 1-3-5: Implement pilot restoration 

techniques for subtidal algal habitats impacted by oil spills or trampling that 

occurred during cleanup activities.

Right:The container ship Cosco 

Busan leaked oil into the bay from a

hole in its hull. 

Oil from the Cosco Busan was 

evident in intertidal and subtidal

areas.
Chapter Three: Science and Cross-Habitat Goals for All Subtidal Habitat Types • 49

Marine Debris

State and local governments spend millions of dollars every year attempting to 

clean up marine debris. Despite decades-long efforts to reduce marine debris 

through cleanup and outreach and education efforts, the proliferation of plastic 

debris continues, in large part due to increased use of single-use plastic products. 

Plastic litter, which comprises up to 60–80% of all marine debris and 90% of 

floating debris, the majority of which comes from land based sources, can last for 

hundreds of years in the environment without ever completely biodegrading. It 

can harm hundreds of marine species, from birds and fish that ingest small pieces 

of debris, to marine mammals that get entangled in fishing gear. The vast majority (80%) of litter reaching the ocean arrives primarily via runoff from land-based 

sources; the remaining 20% comes from ocean-based activities, such as fishing 

and shipping. Some communities throughout California have enacted measures 

to prevent, reduce, and clean up litter before it reaches the ocean, providing successful examples for a statewide effort.

Abandoned and deteriorating vessels are another form of marine debris and 

can have significant and diverse impacts on the bay’s aquatic environment. 

Abandoned vessels may be releasing oil and other pollutants, thereby impairing water quality, impacting wildlife, and posing a human health risk. They also 

decrease public use of intertidal and subtidal habitats and can crush the substrate. Abandoned vessels can have an aesthetic impact that may also result in 

an impact to the economy of a local area (i.e., a marina with several abandoned 

vessels). Finally, abandoned vessels pose a significant navigational hazard, particularly in inclement weather. The long-term outcomes from removing marine 

debris will be to reduce navigational hazards, restore tidal hydrology and habitat connectivity, improve water quality, increase the amount of bay volume and 

surface area, and restore subtidal habitat (eelgrass beds and benthic habitat) for 

use by a variety of aquatic organisms.

Protection goals for subtidal habitat related to marine debris focus on expanding resources to prevent debris from reaching the bay, establishing cleanup programs, removing derelict vessels, increasing pollution prevention infrastructure, and identifying marine debris impacts to subtidal habitats. Restoration 

BCDC has documented more than

400 abandoned vessels that need to

be removed from Richardson Bay and

other areas.
﻿50 • San Francisco Bay Subtidal Habitat Goals Report

goals include surveying sites for marine debris, increasing removal activities, 

conducting pilot projects for creosote pile removal, removing derelict vessels, 

and installing pollution prevention infrastructure.

Marine Debris Control Goal 1

Prevent and capture land or marine sources of trash before 

they enter the bay.

•	 Marine Debris Control Objective 1-1: Install catchment devices that 

trap litter in storm drains and waterways before it enters the bay (e.g., catch 

basins, aquatic debris separators, and trash curtains).

•	 Marine Debris Control Objective 1-2: Place trash and recycling 

receptacles, such as fishing line recycling stations, and educational 

information at boating facilities. (See also Rock Habitats Action 1-1-6).

•	 Marine Debris Control Objective 1-3: Develop subtidal restoration and 

monitoring techniques that minimize the deployment of non-biodegradable 

materials. 

Marine Debris Control Goal 2

Identify, prioritize, and remove large sources of marine debris 

from intertidal and subtidal areas of the bay.

•	 Marine Debris Control Objective 2-1: Survey and map undocumented 

submerged debris, including abandoned boats, fishing gear, and other debris 

for removal.

•	 Marine Debris Control Objective 2-2: Collect data on types of debris 

entering San Francisco Bay. 

Kayaks are used to clean up trash in

the bay.
Chapter Three: Science and Cross-Habitat Goals for All Subtidal Habitat Types • 51

Marine Debris Control Action 2-2-1: Track debris in a centralized database to 

identify potential impacts to the water column and subtidal habitats, and 

pinpoint principal debris sources. 

•	 Marine Debris Control Objective 2-3: Remove existing marine debris 

from the bay.

Marine Debris Control Action 2-3-1: Promote and expand efforts, such as the 

California Coastal Commission’s Coastal Cleanup Program and NOAA’s 

derelict fishing gear removal program to remove intertidal debris (e.g., 

tires, shopping carts, electronic appliances, pieces of creosote pilings) from 

shoreline and wetland areas.

Marine Debris Control Action 2-3-2: Promote and support the US Army Corps 

of Engineers San Francisco District’s debris collection-and-control mission.

Marine Debris Control Action 2-3-3: Promote and support the California 

Department of Boating and Waterway’s Abandoned Watercraft Abatement 

(AWAF) Fund and its vessel surrender program.

Marine Debris Control Action 2-3-4: Remove existing identified abandoned

derelict vessels (approximately 40) from Richardson Bay within 5 years.

Public Access and Awareness

Providing opportunities for people to access subtidal habitats allows the public to discover, experience, and appreciate subtidal habitats in the bay and can 

foster public support for subtidal habitat restoration and protection. However, 

studies indicate that public access may have immediate direct and indirect 

effects on habitats and wildlife. Potential adverse effects on habitat may be 

avoided or minimized by siting, designing, and managing public access to 

reduce or prevent adverse impacts. In addition, providing diverse and satisfying public access experiences can reduce adverse impacts that may result from 

unmanaged, informal access. (See Chapter 11 for more ideas on public involvement and education.)

Public Access and Awareness Goal 1

Increase public awareness and foster support for subtidal 

habitat protection.

•	 Public Access and Awareness Objective 1-1: Provide diverse and 

satisfying access and recreational opportunities for the public to experience 

various subtidal habitats while avoiding or minimizing adverse impacts to 

subtidal habitats.

•	 Public Access and Awareness Objective 1-2: Provide access to natural 

rocky habitats in the bay that encourages appreciation of the habitat and its 

inhabitants while protecting the habitat from trampling.

Elementary school students enjoy an

outing on the bay.

TheWatershed Project uses student

volunteers to monitor habitat.
﻿52 • San Francisco Bay Subtidal Habitat Goals Report

Public Access and Awareness Action 1-2-1: Conduct docent-led tours, and 

place signs at high use rocky intertidal sites to raise awareness about the 

importance of rocky intertidal shoreline areas and ways to avoid impacts 

while visiting these locations. 

Public Access and Awareness Action 1-2-2: Provide sufficient staffing at existing 

protected rocky intertidal areas to inform and educate individuals about 

harmful activities (such as collection of organisms or release of non-native 

species). 

Public Access and Awareness Action 1-2-3: Use durable materials on trails 

and guide rails to reduce erosion of adjacent habitats and to minimize the 

creation of alternate access routes.

Public Access and Awareness Action 1-2-4: Provide diverse and interesting 

access opportunities to reduce the creation of informal access routes.

Public Access and Awareness Action 1-2-5: Develop and place educational 

materials and signs at boating facilities to educate boaters and other 

recreational users about the importance of rock and eelgrass habitats and 

best boating practices in these areas to prevent damage from anchors and 

anchor chains. 

•	 Public Access and Awareness Objective 1-3: Support environmental 

education programs, local museums and nature centers, and schools to 

better integrate current science and subtidal habitat information into 

curriculum and field trip programs.

•	 Public Access and Awareness Objective 1-4: Support hands-on 

involvement and community-based restoration programs that focus on 

San Francisco Bay intertidal and subtidal habitats. Increase coordination 

between academic organizations and non-profit restoration groups to 

create better partnerships in research and restoration projects that involve 

community and student volunteers.

California Conservation Corps

members and volunteers bag clean

Pacific oyster shell donated from

Drakes Bay Oyster Farm.

Volunteers collect data at a native

oyster restoration site.

Save the Bay and other non-profit

groups educate youth on the bay.
 53

CHAPTER FOUR

Soft-Bottom and 

Other Mobile Substrates

More than 90% of the San Francisco Estuary’s bottom is 

composed of particles that are small enough to be moved by tidal 

currents. Soft-bottom habitats include the substrate, organisms living 

on or within the substrate, and the overlying water column. See Figure 4-1. 

Soft-bottom habitat includes sediments that range in size from clay (0.001–

0.0039 mm) to silt (0.0039–0.0625 mm), and sand (0.0625–2 mm). “Mud” 

refers to clay and silt together. All of these particles can readily be moved by 

tidal currents. Larger particles such as gravel (2–64 mm) and cobble (64–256 

mm), are somewhat mobile and are also included in this category. Deposits 

of bivalve shells can be mobile and are also considered in this section. 

Most of the soft sediment in the estuary is fine material (Keller 2009), particularly on shoals. Sand deposits are found throughout deeper parts of the Central 

Bay, the main channel through San Pablo Bay into Carquinez Strait, and parts 

of the Suisun Bay channel (Figure 4-3 in Hanson et al. 2004). Most of this 

material, out to the sill seaward of the Golden Gate, originated within the bay 

and its watershed (P. Barnard, USGS, 2010, pers. comm.). Parts of the Central 

Bay that have been mapped in detail reveal large areas of sand waves (Greene et 

al. 2007), and some deposits of gravel and cobble occur east of the Golden Gate 

(Keller 2009). Apparently all but the larger boulders are moved by very strong 

Pebbles and cobbles on the bottom of 

San Francisco Bay near Angel Island.

An endangered California clapper rail 

takes refuge in cordgrass on intertidal 

mudflats.
﻿54 • San Francisco Bay Subtidal Habitat Goals Report

Figure 4-1: Distribution of Soft-Bottom Habitats in San Francisco Bay.
Chapter Four: Soft-Bottom and Other Mobile Substrates • 55

tidal currents in that region, and flood dominance of bottom currents in parts 

of the cross-section results in sorting of sediments with grain size decreasing 

eastward from the Golden Gate (Keller 2009).

Sandy beaches occur mainly in the Central Bay, but there are far fewer than 

were present historically, and all of the remaining beaches are constrained by 

shoreline development. Benthic surveys in the northern estuary have shown 

sand deposits in the channels, silt to clay elsewhere, and a few shell deposits 

near shore (Hymanson 1991). However, these surveys lack the spatial resolution of the Central Bay mapping. Shell hash from native oysters is found 

in extensive but localized deposits in the South Bay, where it is presumably 

trapped by current patterns. Gravel and cobble are uncommon except in certain areas of the Central Bay.

Conceptual Model for Soft Substrates

Sediment grain size is the key to movement and sorting of sediments and to 

the biological and chemical conditions in the sediments (Figure 4-2 and Figure 4-3). Grain size is largely a function of proximity to sediment sources such 

as rivers and the ocean, and of water movement, which includes waves, tides, 

and tidally-averaged currents. Fine-grained, soft substrate is the most common substrate in most estuaries. Paradoxically, fine-grained sediments are 

Tidal currents 

redistribute and 

sort sediments 

and form sand waves 

in deep channels.

Wind waves stir 

up sediment.

Bat rays, sturgeon, halibut, and other 

animals feed in soft-bottom areas.

Diving ducks eat animals 

in the shallow areas.

Shorebirds feed in the 

intertidal mudats.

Dredging and sand mining stir up 

sediment and remove material and 

organisms.

Shell Hash

Mud provides habitat for 

many benthic invertebrates.

 Microbial processes in layers 

 of sediment chemically trans-

 form nutrients and contaminants.

Corbula

Clams

Sediments wash in from 

rivers during storms.

Figure 4-2: Conceptual 

diagram for soft-bottom 

substrates in the San Francisco 

Estuary. This diagram displays 

key processes that occur in 

and on soft substrates, some 

of the ecosystem services 

these substrates provide, and 

threats to soft substrates.
﻿56 • San Francisco Bay Subtidal Habitat Goals Report

readily kept in suspension by tidal currents and wind-driven waves, but once 

deposited they can become consolidated, sometimes with the aid of organisms 

such as mats of microalgae and biofilm, making them more resistant to erosion 

than sand. This combination results in the establishment and maintenance of 

shoals and mudflats composed of fine sediments, and the bimodal depth distribution of much of the estuary, with its extensive shoals cut by narrow, deep 

channels. The shoals act as a sediment reservoir, storing fine sediments from 

winter floods, which are then resuspended by strong tidal currents and wind 

waves and gradually winnowed out through the dry, windy summer and fall 

(Schoellhamer et al. 2007). The strong current regime makes the San Francisco 

Bay floor a dynamic environment with major bedforms such as sand waves that 

shift in position and shape. Over time, significant alteration of the bay floor 

takes place, and substrate types may move or disappear entirely (Greene 

et al. 2007).

Coarser sediments are confined to high-energy environments where waves 

(beaches and sand bars), river flows (sand deltas), or tidal currents (bay-mouth 

bars, sand waves, channel bottoms) inhibit deposition of finer sediment. Sand 

deposits may also be found where past storms and floods have increased currents temporarily. Sand moves primarily as bedload but can also be transported 

in suspension by strong tidal currents or river flood flows. 

Grain size is critical for the establishment of flora and fauna. Larger sediment particles such as cobble, gravel, or shell, if they remain in place long 

enough, may provide substrate for settlement of organisms otherwise found 

on hard substrates, such as oysters and barnacles, and clams may occupy 

SOFT-BOTTOM SUBSTRATES

Gravel

Available 

Habitat

Benthos

Waves

Water Depth

Tidal and Net 

Currents

Dredging

Sea Level 

Rise

Attribute of physical structure

Threat to habitat

Other inuence on habitat 

Function or species 

inuenced by the habitat

Human-induced threat

Inuence generally causing 

increase in target

Inuence generally causing a 

negative effect upon target

Factor causing either increase 

or decrease in target

Shift among size classes of 

soft substrate 

3541 g. 4-3 soft-bottom

Sand Silt Clay

Forage for 

Birds, Mammals

Habitat

for Fish

Contaminant 

Storage, Release

Water Depth

Net Sediment

Supply

Shipping,

Boating

Processing

of Materials

Sand

Mining

Figure 4-3: Influences on soft substrate, and functions and services provided by soft substrate.

“Available habitat” refers to soft substrate that provides habitat for one or more species.
Chapter Four: Soft-Bottom and Other Mobile Substrates • 57

spaces between cobbles. Fine-grained sediment is generally stable and compact enough to allow many kinds of organisms to reside in or on the sediment. 

Because of its mobility, sand is not a favorable substrate for many benthic 

organisms, and only those well adapted to a transitory environment are found 

there. Mixed sand and mud deposits can be stable enough to support diverse 

benthos (J. Thompson, USGS, 2009, pers. comm.). Some species of fish, notably 

California halibut, occur over sandy bottom, but the exact nature of that relationship is unknown. Juvenile Dungeness crab may use sand waves and formations as transit routes to migrate out to the ocean. 

For some species, the paucity of benthic food resources limits the value of 

sandy habitat. Fine-grained sediment is a key component in estuaries for chemical transformations mediated by microbes, such as nitrogen fixation, denitrification, and oxidation and reduction of metals. Substances in sediments diffuse much more slowly than in the turbulent water column. Microbes oxidize 

organic matter within sediments, and the limited diffusion of oxygen and other 

substances sets up a sharp vertical gradient in oxidation state of the sediments. 

This allows for a variety of microbially mediated oxidation-reduction reactions 

to occur in thin but distinct layers. For example, a vertical profile of activities 

in the sediment proceeds from photosynthesis at the surface to aerobic respiration in the upper, well-oxygenated layer, and then to various kinds of anaerobic 

respiration resulting in denitrification, metal reduction, sulfide and methane 

production, and other processes that create black, sulfurous sediments below 

the sediment surface.

Despite extensive studies, particularly in the last decade, very little is known 

about these microbial activities in the sediments of the San Francisco Estuary. 

In particular, production by benthic microalgae has been estimated only for 

limited areas of mudflat (Guarini et al. 2002). Benthic chemical processes 

and exchange with the overlying water column have been measured in only a 

few studies, most of them limited to South San Francisco Bay (e.g., Grenz et 

al. 2000).

Microbial activity and deposition of organic matter in and on the surface of 

fine-grained sediments support a rich food web of infauna (organisms living 

in the sediment), epifauna (those living on the 

surface of the sediment), and demersal species 

(motile fish or macroinvertebrates associated with 

the sediment surface). The near-surface sediments, their microbial flora, and settled organic 

matter from the overlying water column support 

deposit feeders such as polychaete worms and 

some clams. Filter feeders use the sediment more 

for support than for food, obtaining particles or 

even dissolved organic matter from the overlying 

water column. Many of the macro-organisms 

produce burrows that irrigate deeper sediments, 

A multibeam sonar image of sand 

wave formations on the bottom 

of the bay.
﻿58 • San Francisco Bay Subtidal Habitat Goals Report

altering the positions of the oxidation-reduction zones. Most 

benthic organisms have planktonic larval stages that drift in 

the water for days to weeks before settling to the bottom. Benthic production supports a variety of predators in the overlying 

water column. Predation can disrupt sediments and re-oxygenate near-surface sediments; in shallow waters, bat rays and 

some sharks and other fish disturb the bottom searching for 

food, leaving depressions in the sediment.

Invertebrates living in intertidal to subtidal mudflats support large numbers 

of shorebirds and diving ducks that feed during low tide. The shoals of San 

Francisco Bay are designated by the National Audubon Society as an Important 

Bird Area, a site that provides essential habitat for one or more species of birds; 

these shoals are particularly important to diving ducks. 

To summarize, interactions between the water column and the sediment are 

strong. They occur through physical (settlement and resuspension), chemical (transport and transformation of byproducts of microbial activity), and 

biological processes (feeding and burrowing by benthic and water-column or 

demersal organisms, production and settlement of larvae).

Species Composition

As in most estuaries, the soft bottom harbors most of the San Francisco Estuary’s 

benthic organisms (Schaeffer et al. 2007) but probably not most of its species. 

Benthic species composition is highly variable and depends on 

water depth, sediment grain size, and position along the estuarine salinity gradient. Most of the species of the soft-bottom 

benthos are introduced, and species composition is highly variable in time and space (Nichols and Thompson 1985). Species 

composition at any one location is largely determined by the 

overlapping distributions of the species in salinity space (Schaeffer et al. 2007, Figure 35 in Kimmerer 2004). Distributions of 

benthic organisms shift as the salt field moves in response to 

changing freshwater flow. For example, when the salt field moves landward during a dry period, a region that was once fresh becomes brackish. Freshwater 

organisms die or fail to settle in this region, and more salt-tolerant species, previously excluded by low salinity, begin to settle there. The reverse happens with an 

increase in freshwater flow. In both cases it can take months after the die-off of 

the initial group of organisms for the new group to settle and grow. During these 

periods, regions of the estuary are left depauperate (Nichols 1985). 

The introduced overbite clam Corbula amurensis seems to be an exception to 

the above pattern, as it is found in all salinities from oceanic almost to freshwater, where its distribution overlaps with that of the introduced freshwater clam 

Corbicula fluminea. Filtration by these clams has an overwhelming influence 

on the plankton of the overlying water (Alpine and Cloern 1992, Thompson 

2005, Lopez et al. 2006).

Bat ray on sand.

Green sturgeon.
Chapter Four: Soft-Bottom and Other Mobile Substrates • 59

Benthic organisms support many demersal fish, including recreationally 

important species (e.g., California halibut, striped bass) and threatened species such as green sturgeon. Some demersal fish such as bat rays forage on 

mudflats at high tide. Numerous bird species forage in shallow soft substrate, 

including diving ducks (canvasback, greater and lesser scaup, surf scoter). The 

San Francisco Estuary is a key stop on the Pacific Flyway for ducks and shorebirds, which forage in salt ponds and intertidal mudflats (Warnock et al. 2002). 

Marine mammals forage on the bottom (gray whales) or consume demersal 

and pelagic fish (seals, sea lions).

Sediment Budgets

Several attempts have been made to estimate sediment budgets for the estuary, 

summarized by Cohen (Appendix 2-1) and McKee et al. (2006). About 57% of 

the sediment load to San Francisco Bay comes from the Central Valley (McKee 

et al. 2006), the rest entering the bay from local watersheds and the ocean. 

Most of the sediment budgets have not distinguished among particle sizes, so 

determining budgets for subsets of the sediment pool (e.g., sand, or individual 

basins) will be difficult. In particular, sediment supply from the rivers is probably important to the sand budget only during high-flow years, and then only 

if bedload transport is included in the estimate. Schoellhamer et al. (2005) 

constructed a sediment budget and estimated the import of sand from the 

coastal ocean at about 5.5 million cubic meters per year, but more recent work 

shows that the sand sill outside the Golden Gate is probably of estuarine and 

watershed origin (P. Barnard, USGS, 2010, pers. comm.). Sediment deposits in 

the bay are replenished largely by the major rivers, with some sediment coming 

A subtidal slough meanders through 

a mudflat.

Harbor seal.

Gray whale.
﻿60 • San Francisco Bay Subtidal Habitat Goals Report

from the coastal ocean as well as local tributaries and erosion. The 

entire sedimentary system of the estuary and its watershed underwent a substantial alteration due to a large increase in sediment 

from hydraulic mining in the watershed in the late 1800s. The 

sediment budget for the estuary may still be out of equilibrium 

because of this historical modification (Jaffe et al. 2007, Hanes and 

Barnard 2007). The influx of sediment during hydraulic mining 

caused shoaling in much of the estuary, but much of the excess 

material has since eroded away.

The present sediment budget is uncertain, but erosion of mudflats 

and shoals is likely to continue because of reduced sediment supply 

due to water control structures, damming of rivers (Appendix 2-1, 

Wright and Schoellhamer 2004, McKee et al. 2006), and the loss of 

the large pool of sediment from hydraulic mining (Jaffe et al. 2007, 

Schoellhamer 2009). One result of decreased sediment supply is 

likely to be loss of mudflats, possibly accelerated by the capture of 

intertidal areas by the invasive hybrid cordgrass (Neira et al. 2006). 

In addition, the supply of sand from the rivers has been greatly 

reduced, and aggregate mining likely exceeds the supply rate, resulting in an ongoing loss of sand from the estuary.

Threats to Soft Substrates

Threats to the soft-bottom communities are numerous; although many are 

localized, their overall impacts may be large (see Figure 4-4). Dredging and 

dredge material disposal associated with shipping and boating disturb the 

bottom periodically in relatively small areas of the estuary. Wakes from ships 

and ferries can accelerate erosion of shoals. Construction in or adjacent to the 

estuary, for example, for bridges, piers, and harbors, causes short-term disruption. Permanently installed structures displace the benthic habitat and cause 

long-term alteration of patterns of sediment movement and deposition. All of 

these activities can disrupt the functions of the soft bottom by killing or removing organisms, mixing the sediments, and disrupting the layers of different 

oxidation conditions. More broadly, activities that alter sediment transport and 

deposition, current patterns, or salinity distributions can disrupt soft-bottom 

communities. Globally, the most pervasive harm to these communities arises 

from hypoxia due largely to eutrophication, which has not been an issue in this 

estuary for several decades (see Chapter 3, Water Column).

Contaminants

Contamination by chemical substances is widespread in sediments in the 

estuary (e.g., Oros et al. 2007) with some areas identified as contaminant “hot 

spots.” Contaminants are a particular issue for soft substrates for several reasons. First, many organic compounds and metals bind to fine-grained sediments and are available for transfer up the benthic food web. Second, contaminants (e.g., mercury, silver, DDT) can be stored in sediments long after their 

A sand barge near the Port of 

San Francisco.

The Port of Oakland’s Inner Harbor

50' deepening project.
Chapter Four: Soft-Bottom and Other Mobile Substrates • 61

Figure 4-4: Locations of Soft-Bottom Habitat Stressors in San Francisco Bay.
﻿62 • San Francisco Bay Subtidal Habitat Goals Report

inputs to the estuary have been stopped. Third, metals in the sediments can be 

reduced to soluble forms by microbial activity, increasing their bioavailability. 

Finally, the erosion in some areas due to sediment imbalance may be resuspending deeper sediments with their contaminant loads into the water column, 

making the contaminants available to the food web. Chemical contamination 

can significantly disrupt survival, fitness, or reproductive success of various 

organisms including fish (Ostrach et al. 2008) and birds (Takekawa et al. 2002, 

Ackerman et al. 2008). In addition, sediment-bound contaminants such as 

mercury, PCBs, and organic compounds can be concentrated in the food web, 

resulting in concentrations in fish that prompt warnings to limit consumption 

by humans. Contamination identified in testing can limit the utility of dredged 

material for wetland restoration and other purposes. Emerging contaminants 

such as endocrine disruptors may have ecological effects although the importance of sediments as reservoirs for these contaminants is less clear than for the 

other substances mentioned above.

Benthic Disruption/Removal

Mining for sand occurs under several leases in the Central Bay, and Suisun Bay 

(Hanson et al. 2004). During March 2002–February 2003 about 1.3 million 

cubic meters was mined, mostly from the Central Bay (Hanson et al. 2004). The 

relationship of this volume of sand to either the extant quantity of sand or the 

sand supply rate is being investigated (P. Barnard, USGS, 2009, pers. comm.). 

There is evidence of net loss of 14 million cubic yards of sand between 1997 

and 2008 in lease areas in Central Bay (P. Barnard, USGS, 2009, pers. comm.). 

Potential environmental effects of sand mining were reviewed by Hanson et al. 

(2004). These include entrainment of water column and benthic organisms in 

the dredge suction, impacts associated with the sediment plumes, and removal 

of benthic habitat. Entrainment of water column organisms probably has a 

Maintenance dredging at the Port of 

Richmond.
Chapter Four: Soft-Bottom and Other Mobile Substrates • 63

minor impact because of its small scale. The volume of water ingested by the 

sand dredges is around three to four times the volume of the sand mined (Hanson et al. 2004), which amounts to about 0.1% annually of the volumes of the 

estuarine basins where sand mining occurs. Sediment plumes are unlikely to 

have lasting effects given the high background turbidity; dredging plumes were 

found to have only a localized effect (Schoellhamer 2002). The scale of the loss 

of benthic organisms is unknown mainly because their abundance in sandy 

areas is unknown. Since the lease areas are well-delineated, a comparative study 

between lease and non-lease areas could be conducted to help resolve whether 

substantial resources are being lost through sand mining. 

Areas of shell hash, particularly in the South Bay, have also been mined for 

industrial uses of the shell, leaving large depressions that are clearly visible on 

sonar records. The impact of current and historical mining on the amount of 

shell deposits and on benthic biota is unknown; however, historic mining has 

resulted in changes to bathymetry (Jan Thompson, USGS, 2009, pers. comm.).

Rationale for Establishing Goals for Soft Substrates

The approach outlined in Chapter 2 leads to the conclusion that soft-bottom 

habitats are perhaps threatened by decreasing sediment supply, locally by the 

effects of dredging and sand mining, and by various contaminants. However, 

since there is no real opportunity for increasing the quantity of these habitats, 

the best we can do is to improve their quality and manage them properly.

The soft-bottom habitats that are of principal concern, in terms of persistence 

and maintenance, are intertidal and subtidal mudflats, which are threatened by 

erosion and encroachment of cordgrass. The term “mudflat” is used below to 

include both subtidal and intertidal areas. Loss of mudflats will likely be accelerated by sea level rise if the rate of rise exceeds the rate of sediment accumulation or wave action increases because of hardened shorelines. Increases in ferry 

travel on the bay would increase erosion along soft shorelines due to wakes. 

There is no obvious mechanism for protecting mudflats, so some consideration 

might be given either to establishing buffer zones or other methods to minimize the impact of wakes in important mudflats, or to manipulating sediments 

to encourage growth and maintenance of mudflats.

The ecological benefits of mudflats in the estuary have not been quantified, 

although large numbers of birds are observed to forage there. The relationship 

between quantity of mudflat and the numbers or distribution of various bird 

species, and use of the mudflats by other groups of organisms, would need to 

be determined to support informed choices about protection of these areas. 

A better understanding of both the function of sand habitats and the effect of 

sand mining on subtidal or intertidal habitats is needed to better manage sand 

habitat in the bay.

Goals for soft sediment habitats focus on protection, including reducing effects 

of contaminants and bottom disturbance, preventing loss of mudflats and 

Intertidal and subtidal mudflats

support many resident and migrant 

shorebirds.

Invasive cordgrass threatens 

mudflats.
﻿64 • San Francisco Bay Subtidal Habitat Goals Report

beaches, and improving our understanding of ecosystem services and threats 

to this habitat as well as our ability to protect it. Other goals and objectives are 

intended to reduce impacts from existing known contaminants, so that they 

are not contributing to bioaccumulation in fish, birds, or mammals. Intertidal 

mudflats and sand beaches are of particular concern because of their habitat 

value for various fish and birds, and because of long-term threats to their existence. Protection goals should not limit creation of other desirable habitats 

(e.g., eelgrass beds, native oyster beds) within existing soft sediment habitats. 

As soft bottom sediments are by far the most abundant subtidal habitat type in 

San Francisco Bay, conversion to eelgrass or shellfish beds at appropriate sites 

is encouraged.

Science Goals for Soft Substrates

Soft Substrate Science Goal 1

Understand the extent of ecosystem services provided by softbottom habitats. 

Question A. How important are mudflats in the life cycles of birds and other 

organisms that use them? 

What would be the impact on the bird or fish populations of a substantial 

loss of mudflats? At present, bird populations may be limited by conditions in 

remote locations, but if the local habitat shrinks and alternatives are not available, mudflat area could become the chief limiting factor to bird populations. 

Alternatively, birds and fish may simply forage elsewhere.

Question B. What is the distribution of various sediments by size and depth 

throughout the estuary?

A better set of sediment maps for the parts of the estuary not already thoroughly surveyed would help to assess conditions and define actions. These 

maps would have to be updated periodically to account for erosion and 

deposition. 

Question C. What is the overall sediment budget for the estuary and its major 

basins, and the relationship of sand removal to sand supplies?

A better grasp of the estuarine sediment budget would be useful both for projecting long-term changes in sediment distributions and for placing sand mining in context. An understanding of the sand budget for mining lease areas is 

essential for effectively managing the mining activities. 

Question D. What is the spatial extent of shell deposits and what services do they 

provide?

There is no information on the importance of shell deposits as habitat, and little 

information on their spatial extent.
Chapter Four: Soft-Bottom and Other Mobile Substrates • 65

Question E. What is the ecological value of intertidal and subtidal sand deposits?

These deposits are important in beach formation, but their ecological value is 

poorly known.

Question F. What are the species composition of the benthos, key functions occurring in the soft sediment, and ecosystem services supported by soft sediment?

This applies to all depths and grain sizes. Although much of the emphasis 

for management is on sand mining areas and mudflats, the deep soft-bottom 

habitat comprises much of the estuary’s area and is therefore likely to be far 

more important in supporting ecosystem services than other habitat types that 

occupy small areas.

Soft Substrate Science Goal 2

Understand the threats to mudflats and other soft-bottom 

habitats.

Question A. How are individual mudflats changing over time, and what is causing them to change?

To predict the fate of individual mudflats requires knowledge of sediment 

budgets at basin and sub-basin scales, and also the short-term, local processes 

of deposition and wind- and current-driven resuspension. Encroachment of 

cordgrass and restoration of salt ponds are both localized and quantifiable, and 

determining their influence on mudflats should therefore be tractable. Furthermore, local vertical movement due to seismic activity may alter sea level relative to the elevation of mudflats. A long-term monitoring program of rates of 

change in area and elevation of mudflats would be valuable.

Question B. How and why do mudflats differ regionally in their support of species 

such as shorebirds and bottom-feeding fish? 

A decline in extent of mudflats in one region may result in a behavioral shift 

of these species to other regions, but only if other conditions are suitable. 

Shorebirds feed on intertidal and 

subtidal mudflats.
﻿66 • San Francisco Bay Subtidal Habitat Goals Report

Therefore, knowing the use of different regions and the underlying motivations 

behind those specific uses would help in understanding the likely responses to 

changes in mudflat extent.

Question C. Is it feasible to construct simulation models of the formation and erosion of mudflats?

Improved hydrodynamic models of the estuary provide useful predictions of 

conditions under alternative scenarios of inflow, bathymetry, and sea level. 

However, modeling sediments is considerably more difficult than modeling the 

movement of water. Modeling scenarios may be feasible, but predictive modeling seems beyond our current reach because of the difficulties in estimating 

coefficients for deposition and erosion. 

Question D. What are the broad-scale impacts of sand and shell mining and 

dredging on sediments and on estuarine biota?

Management of these habitats requires knowledge of local and estuary-wide 

impacts to gauge the cumulative impacts of sand and shell mining, including 

the effects of persistent borrow pits left after removal of material, and the contributions of individual mining leases to these impacts. 

Question E. What is the recovery time of the benthos from disturbance?

This information is essential for answering the previous question. Most impact 

assessments focus only on the immediate impact, but disturbances could persist.

Sand beaches and offshore sand shoals provide roosting habitat for birds.
Chapter Four: Soft-Bottom and Other Mobile Substrates • 67

Soft Substrate Science Goal 3

Determine suitable methods for protecting mudflats and 

beaches.

Question A. What methods are available for protecting mudflats and beaches, 

and how effective are they?

An initial review of the available information on engineering long-term solutions to mudflat and sand beach loss should be the first step in answering this 

question. Depending on the results of such a review, experimental manipulations might be considered to test alternative approaches using adaptive management over the long term.

Question B. How do mudflats in different parts of the estuary differ in their sensitivity to change, and in their support of the ecosystem services that are at risk?

If ways to protect mudflats are available, it is essential to determine which 

mudflats provide the most support for desired ecosystem services, which are at 

high risk of loss or degradation because of changing sea level, erosion, or other 

threats, and which can be protected most effectively.

Soft Substrate Science Goal 4

Understand the magnitude of the ecological risks posed by 

contaminants bound to the sediments.

Question A. What are the distributions and concentration of various contaminants in estuarine sediments?

Contaminant concentrations are an important consideration for management 

of sediments in the estuary. Decisions about dredging, dredge disposal, and 

removal of artificial habitat, which may disturb sediment-bound contaminants, 

must be made with knowledge about the contaminants likely to be released. 

However, developing maps of the distributions of contaminants may not be 

cost-effective beyond what is already being done by the Regional Monitoring 

Program. Individual contaminant measurements are expensive, and distributions can be very heterogeneous spatially, and temporally variable as sediments 

move around. Therefore, site-specific investigations may be more cost-effective 

than attempting to develop general maps of contaminant distributions.

Question B. What ecological risks (distinct from risks to human health) do these 

contaminants pose?

Mercury and selenium from the environment have been shown to impair 

the health of organisms in higher trophic levels such as birds and some fish. 

However, knowledge of the risks of some other contaminants, and particularly 

multiple contaminants, is not well developed. As with questions about distribution, answers to this question may be more specific to certain locations and 

contaminants, rather than broad and general.
﻿68 • San Francisco Bay Subtidal Habitat Goals Report

Protection Goals for Soft Substrates

Soft Substrate Protection Goal 1

Consider the potential ecological effects of contaminated 

sediments when developing, planning, designing, and 

constructing restoration projects or other projects that 

disturb sediments. 

•	 Soft Substrate Protection Objective 1-1: Identify and prioritize 

ecological risks associated with contaminated sediments in the estuary. 

Soft Substrate Protection Action 1-1-1: Work with the appropriate agencies 

to identify and prioritize ecological risks associated with contaminated 

sediments and locations where priority risks occur within the estuary. 

Soft Substrate Protection Action 1-1-2: Work with the appropriate agencies to 

develop a sampling protocol to assist interested parties in delineating the 

extent of contaminated sediments that may pose an ecological risk at nondredging sites. 

•	 Soft Substrate Protection Objective 1-2: Develop an effective solution 

to address contaminated sediments that are determined to pose an 

ecological risk. 

Soft Substrate Protection Action 1-2-1: Collaborate with the appropriate 

agencies to develop a simplified regulatory process for voluntary cleanups.

Soft Substrate Protection Action 1-2-2: Develop funding sources to support 

delineation of contamination, planning, and contaminant removal.

Soft Substrate Protection Action 1-2-3: Provide funding for and development of 

regional multi-user rehandling and disposal facilities for contaminated bay 

sediments. 

•	 Soft Substrate Protection Objective 1-3: Work collaboratively on 

monitoring and prioritizing emerging contaminants of concern and 

relevant protocols and policies that may impact bay sediments, and restoration or other projects.

Soft Substrate Protection Action 1-3-1: Promote discussion of emergent 

contaminants affecting soft substrates and research needs at existing annual 

or semiannual forums including the State of the Estuary conference, Dredge 

Material Management Office’s annual meeting, and Regional Monitoring 

Program annual meeting.

Soft Substrate Protection Action 1-3-2: Develop stable funding sources 

to continue the joint NOAA/State Water Resources Control Board 

mussel watch data collection and early detection of emerging pollutants 

pilot project.
Chapter Four: Soft-Bottom and Other Mobile Substrates • 69

Soft Substrate Protection Goal 2

Promote no net increase in disturbance to San Francisco Bay 

soft bottom habitat. 

•	 Soft Substrate Protection Objective 2-1: Minimize bottom disturbance 

in the bay.

Soft Substrate Protection Action 2-1-1: For new construction projects, 

encourage placement in appropriate areas, such as areas of low 

sedimentation. 

Soft Substrate Protection Action 2-1-2: For projects involving reconfigurations 

of existing structures, encourage placement of project components in a way 

that avoids or minimizes the need for dredging.

•	 Soft Substrate Protection Objective 2-2: Minimize placement of 

structures in subtidal and intertidal soft bottom habitats of the bay. (See 

Artificial Structures, Chapter 6, and discussion of how to minimize impacts 

from restoration and living shoreline projects in Chapters 3, 7, and 8).

Soft Substrate Protection Goal 3

Promote no net loss of San Francisco Bay subtidal and 

intertidal sand habitats.

•	 Soft Substrate Protection Objective 3-1: Continue the efforts of the 

interagency sand mining working group to encourage harvests of sand at 

levels replenished through natural processes.

Soft Substrate Protection Goal 4

Develop a coordinated, collaborative approach for regional 

sediment management for San Francisco Bay.

•	 Soft Substrate Protection Objective 4-1: Promote riparian restoration 

techniques that provide for sediment storage capacity in stream and wetland 

systems while allowing for excess sediment to be transported to the bay 

through natural hydrogeomorphic processes. 

•	 Soft Substrate Protection Objective 4-2: Develop and promote flood 

control methods, including floodplain restoration, that nourish marshes 

from the watershed. 

•	 Soft Substrate Protection Objective 4-3: Promote beneficial reuse of 

suitable dredged sediment in habitat restoration/beach nourishment projects.

Soft Substrate Protection Action 4-3-1: Determine storage and stockpile 

locations for dredged sand for later beneficial reuse. Develop restoration 

projects that are in close proximity to dredging projects.

Three-dimensional images show 

long-term changes in the soft 

bottom of San Pablo Bay.
﻿70 • San Francisco Bay Subtidal Habitat Goals Report

Soft Substrate Protection Action 4-3-2: Identify funding sources and facilitate 

transport of mud and sandy material from maintenance dredging projects to 

areas needing sediment, including in areas using the Reef Ball© technique associated with native oyster and living shoreline restoration (see Chapters 7, 10).

Restoration Goals for Soft Substrates

In developing restoration goals for sand beaches, existing efforts to increase sand 

beach protection and restoration, including those described in “Prospects for 

San Francisco Bay Beach Expansion” (Baye 2007, unpublished) were considered.

Soft Substrate Restoration Goal 1

Encourage the application of sustainable techniques in sand 

habitat replenishment or restoration projects.

•	 Soft Substrate Restoration Objective 1-1: Promote sand beach creation, 

restoration, and replenishment projects that use clean, maintenance-dredged 

sand where possible and in areas where sand is deposited, such as at the 

river delta interface. See Figure 4-5.

•	 Soft Substrate Restoration Objective 1-2: Consider incorporating living 

shoreline techniques to retain sand, either from natural deposition or from 

sand replenishment.

Sand Replenishment Project Examples Project Contact

Crown Beach in Alameda East Bay Regional Park District

Vincent Park in Richmond Bob Battalio, PWA

Pier 94 Sand Nourishment Project Roger Leventhal, FarWest Restoration 

Engineering

Soft Substrate Restoration Goal 2

Encourage removal of artificial structures that have negative 

impacts on soft bottom habitat function. (See Artificial 

Structures, Chapter 6).

Potential sand

beach creation, 

restoration, and

replenishment sites

• Eastshore State Park, 

including Albany Beach

• Pt. Isabelle Regional Shoreline,

Albany and Richmond

• Pt. Pinole Regional Shoreline,

Pinole

• San Rafael shoreline

• San Leandro 

Regional Shoreline

• Hayward Regional Shoreline

• San Francisco 

southeastern shoreline

• Coyote Point
Chapter Four: Soft-Bottom and Other Mobile Substrates • 71

Figure 4-5: Suggested locations for pilot intertidal sand beach enhancement 

and living shorelines.

 73

CHAPTER FIVE

Rock Habitats

Relatively little hard substrate occurs naturally in the 

estuary, owing mainly to the vast quantities of fine sediment that have 

been deposited by the rivers. Rock habitat is one class of hard substrate, 

the other being artificial structures (Chapter 6). Rock habitat in this chapter 

encompasses boulders to bedrock; that is, rock that is not normally moved 

by currents.

Rock habitat occurs mainly as scoured low-relief bedrock in the deep, narrow channels where the estuary passes through the Coast Range and as bedrock outcrops and boulders in the areas of the Central Bay where currents are 

strong. Many rock outcrops, especially those near the entrance to San Francisco Bay, have been lowered by blasting to reduce the hazards they present to 

ships, and they may be lowered further as ships with greater draft are built (Sea 

Surveyor 2000). See Figure 5-1. Some rock outcrops are flat-topped and are 

surrounded by boulder fields, presumably a result of previous blasting (Garcia 

and Associates 2001, Chin et al. 2004). 

A kayaker navigates over rocky subtidal habitat.
﻿74 • San Francisco Bay Subtidal Habitat Goals Report

Figure 5-1: Distribution of Rock Habitats in San Francisco Bay.
Chapter Five: Rock Habitats • 75

Conceptual Model for Rock Habitats

Rock substrates alter flow fields, distorting patterns of sedimentation and altering surrounding soft-bottom habitat (Appendix 2-2; Figures 5-1 and 5-2). Once 

a bacterial film has been established, submerged rock can be colonized by a 

variety of organisms. These organisms include attached algae and animals such 

as sponges, bryozoans, tunicates, hydrozoans, anemones, barnacles, mussels, 

and oysters. Numerous other invertebrate animals (for example, amphipods, 

isopods, crabs) and fishes (for example, prickly sculpin, rockfish) reside on, 

under, or near areas of hard substrate, using rocky habitats for protection or 

food supply.

Some fish species such as rockfish use alterations in the tidal flow field caused 

by irregularities of bottom topography, including rocky substrate, to their 

advantage in feeding. Some fish (for example, sculpin) reside among hard 

substrate features, and their association with these features may be obligatory or opportunistic. Some species, notably Pacific herring but also some 

invertebrates, use rock and other hard substrate as well as attached vegetation 

for spawning. Other fish and invertebrates found around hard substrates, for 

Current speeds are reduced by rock 

outcrops.

Invertebrates such as bryozoans, 

tunicates, anemones, and sponges, 

as well as algae, use rock outcrops 

as habitat.

Rock outcrops are used as habitat by

rocksh and other shes.

Herring spawn on rock outcrops.

Oil spills can damage rock habitats.

Figure 5-2: Conceptual diagram for rock habitat in the San Francisco Estuary.This diagram

displays key processes that occur in and on rock, and some of the ecosystem services these

substrates may provide.

West Marin Island in the Marin 

Islands NationalWildlife Refuge

provides critical nesting area for

egrets and herons.
﻿76 • San Francisco Bay Subtidal Habitat Goals Report

example, pelagic fishes such as anchovy, are equally abundant elsewhere. Birds 

use exposed sections of hard substrate for resting and nesting, and seals and sea 

lions also rest on them at low tide.

Because most rock outcrops occur in saline water within a tidal excursion of 

the Golden Gate, species composition of the flora and fauna should be similar 

to those on other extensive rocky subtidal habitats along the Central California coast. Detailed species composition of animals has not been determined 

for bay rock outcrops although video and photographs taken from a remotely 

operated vehicle (ROV) identified several species also found commonly outside the bay (Garcia and Associates 2001). The bay outcrops were covered with 

a “turf ” of sessile organisms including bryozoans, tunicates, anemones, and 

sponges. Rocky shores are confined to a few areas near the Golden Gate, and 

may also harbor organisms found in similar sites on the outer coast.

A total of 162 species of attached algae have been reported from surveys within 

the estuary, most attached to hard substrate; of these, most were species also 

found on the open coast. Thirty-three species classified as estuarine were found 

mostly on artificial substrate (Josselyn and West 1985). 

Threats to Rock Habitats

Blasting to remove or deepen outcrops for safety of navigation is a significant 

threat to rocky habitats. Potential threats also exist from sediment deposition 

and, for intertidal rock, oil spills and trampling by humans. Colonization by 

invasive species is also a threat to these habitats. See Figure 5-3, and Chapter 3. 

Rationale for Establishing Goals for Rock Habitats

Applying the approach outlined in Chapter 2 (Figure 2-1), it is clear that rock 

habitats support valued ecosystem services and are in short supply in the estuary (Figure 5-3). However, restoration of rock habitat in the sense of providing 

more of it seems impracticable. This directs our attention to protection and 

maintenance rather than restoration. There are restoration methods directed at 

the biota associated with rock habitat but those are primarily discussed in the 

shellfish, macroalgal, and living shoreline sections.

Historic photo of rock blasting to

remove navigational hazards inside

the Golden Gate.

Seals rest on rocks at the Brothers

Islands near Point Molate in 

Richmond.
Chapter Five: Rock Habitats • 77

Figure 5-3: Locations of Rock Habitat Stressors in San Francisco Bay.
﻿78 • San Francisco Bay Subtidal Habitat Goals Report

The increase in size and draft of vessels using San Francisco Bay could require 

further deepening of the channels and blasting of the rock outcrops (Carlson et 

al. 2000) to provide safe navigation. It would be useful to know which species 

are using these habitats to assess the environmental impacts of any proposed 

blasting. In the interim while waiting for the data based on the research questions, our recommendation is to protect these rock outcrops as much 

as possible.

Goals for rock habitat focus on protecting existing intertidal and subtidal 

rock from being removed for vessel traffic and damaged by public access; 

on enhancing this habitat by removing invasive species and debris; and on 

improving our understanding of the ecosystem services this habitat provides 

and the species that utilize rock habitats. 

Science Goals for Rock Habitats

Rock Habitats Science Goal 1

Understand the ecosystem services provided by rock habitats 

and the species dependent on them. 

Question A. What lives on the rock outcrops, and in what abundance?

Without knowing what is there, it is difficult to say what would be lost by further deepening of the outcrops. By knowing which species are present and how 

abundant they are it should be possible to estimate the relative value of these 

habitats. In particular, the presence of or potential for re-establishing endangered, special-status, or important fishery or forage species known to associate 

with rock outcrops should be determined.

ROCKY SUBSTRATE

Available 

Habitat

Spawning

Removal

Attribute of physical structure

Threat to habitat

Function or species 

inuenced by the habitat

Inuence generally causing 

increase in target

Inuence generally causing a 

negative effect upon target

Factor causing either increase 

or decrease in target 

3541 g. 5-3 rocky

Desired

Species

Introduced 

Species

Burial

Soft-bottom

Habitat

Sediment

Distributions

Current

Velocities

Figure 5-4: Influences on rocky habitat, and functions and services provided by submerged rock.

“Available habitat” refers to rocky substrate that provides habitat for one or more species.
Chapter Five: Rock Habitats • 79

Question B. What lives on rocky shores, and in what abundance?

Although these sites are much more visible (and visited) than rock outcrops, 

little information on species composition has been published. Such information would help us understand what can be gained by protecting these habitats.

Rock Habitats Science Goal 2

Understand the ecosystem services provided by restored rock 

habitats.

Question A. What are the ecological consequences or benefits of using quarried 

rock in restoration?

Quarried rock may be used for restoration and shoreline protection as sea level 

rises. It is important to understand how rock habitat placed through restoration 

actions functions relative to existing, natural rock habitats.

Protection Goals for Rock Habitats

Rock Habitats Protection Goal 1

Promote no net loss of natural intertidal and subtidal rock 

habitats in San Francisco Bay.

•	 Rock Habitats Protection Objective 1-1: Promote preservation of

natural rock habitats in the bay by minimizing removal or lowering of rock 

pinnacles and outcrops. 

•	 Rock Habitats Protection Objective 1-2: Provide access to natural 

rock habitats in the bay that encourages appreciation of the habitat and 

its inhabitants while protecting it from human trampling. See additional 

actions under Chapter 3, Public Access and Awareness section.

Above: Rocky intertidal shoreline

extends to rocky subtidal habitat. 

Rocky intertidal shoreline provides

habitat space for seaweeds, oysters,

and other invertebrates.
﻿80 • San Francisco Bay Subtidal Habitat Goals Report

Restoration Goals for Rock Habitats

Rock Habitats Restoration Goal 1

Restore and maintain natural intertidal and subtidal rock 

habitats in San Francisco Bay.

•	 Rock Habitats Restoration Objective 1-1: Remove invasive species from 

San Francisco Bay that may impact rocky intertidal habitats (see Chapter 3, 

Invasive Species section, Undaria and Ascophyllum). 

•	 Rock Habitats Restoration Objective 1-2: Provide funding and 

programs to clean up and prevent debris and derelict equipment at boating 

facilities (such as installing fishing line recycling stations) and upland sites 

adjacent to or within rock habitat. (See Chapter 3, Marine Debris). 

•	 Rock Habitats Restoration Objective 1-3: Incorporate living shoreline 

techniques to enhance the function of existing natural rock (see Chapter 10, 

Living Shoreline section).

Ochre star in the rocky intertidal zone.
 81

CHAPTER SIX

Artificial Structures

Artificial structures are found throughout the estuary and 

therefore are exposed to the full range of estuarine conditions, in 

particular to all salinities. Artificial structures include a wide variety 

of human-built objects, mainly associated with development, and discarded 

objects (Figure 6-1). Artificial structures were built to protect shorelines and 

shoreline structures (seawalls, jetties, revetments), for transportation (bridge 

and pier pilings, wharfs, moorings, wrecks, derelict vessels, the reserve or 

“mothball” fleet in Suisun Bay) and recreation (fishing piers, boat ramps, 

marinas, duck blinds), to support industry (shore-side buildings, water intakes 

or outfalls, transmission towers, pipelines, cables), and more recently for 

restoration (oyster shell and artificial reef structures). Artificial structures 

(Figure 6-2) are similar to rocky habitats in that they alter local wave and 

current patterns and provide physical habitat for a variety of species. However, 

artificial structures differ from rocky habitats in their spatial distribution in 

the estuary, and contain structural features that do not occur on rock outcrops. 

Thus, the fish and invertebrate assemblages on natural rocks may differ from 

those on artificial substrates. 

Sunken marine debris encrusted with algae and invertebrates provides artificial habitat for fish.
82 • San Francisco Bay Subtidal Habitat Goals Report

Figure 6-1: Distribution of Artificial Structures in San Francisco Bay.
Chapter Six: Artificial Structures • 83

The potential removal of abandoned structures for aesthetic or practical 

reasons is of particular interest. Although artificial substrates function as 

habitat for many organisms such as herring, some substrates are potentially 

toxic. The removal of structures offers an opportunity for adaptive 

management, serving to answer questions about how structures in general 

affect the habitat and how this effect varies with structural material, size, shape, 

and location. On the other hand, the value of artificial structures as habitat may 

exceed the advantages of removing them, as discussed below.

Conceptual Model for Artificial Structures

Like rocky substrates, artificial structures alter wave patterns and flow fields, 

induce local scouring and deposition of sediment, and provide physical habitat 

(Appendix 2-2; Figures 6-2 and 6-3). Sessile organisms such as mussels and 

oysters use both habitats for attachment, and artificial structures provide refuge 

Current speeds are reduced by articial structures.

Toxic creosote is present in pier pilings.Toxins are 

released from other structures.

Invertebrates, mostly introduced, such as bryozoans, 

tunicates, anemones, and sponges, as well as algae, 

use articial structures as habitat.

Herring spawn on articial structures but 

 embryo survival may be low.

Active piers are used for shipping and shing.

Shading from piers oers 

protection for sh and reduces

light for plants.

Figure 6-2: Conceptual diagram for artificial structures in the San Francisco Estuary. This 

diagram displays processes that occur in and on artificial substrates.
84 • San Francisco Bay Subtidal Habitat Goals Report

and foraging areas for various organisms including fish, resting and nesting 

sites for birds, and haulouts for seals and sea lions. 

However, these two habitat types differ in their distribution within the estuary. 

For example, some artificial structures such as rock jetties and revetments 

(riprap) may provide habitat resembling natural rock but were installed in 

locations that would not naturally have much rock. Since hard substrate is 

naturally in short supply in fresh to brackish regions of the estuary, it is likely 

that few native species in these regions are obligate users of hard substrate. 

Rather, most of the organisms found on artificial structures are not native to 

the estuary (Appendix 2-2). In addition, the placement of artificial substrates 

can differ from that of rock outcrops. Artificial structures may be isolated from 

the shore or the bottom or continuously exposed to surface conditions, and can 

shade the bottom (Appendix 2-2). These differences imply a different habitat 

value from that of natural rock outcroppings and boulders.

Structures can affect local wave and current patterns mainly by introducing 

additional friction. This reduces current speeds and breaks up waves, causing 

deposition of sediments in some areas and scour in others. When structures 

change the movement of sediment, coastal erosion may result in some places 

while other areas may need to be dredged. Walls and revetments in particular, 

designed to protect shorelines, can shift the focus of erosion to other nearby 

locations. Generally the effects of these structures on waves and currents are 

localized, so removing the structures may increase current speeds and wave 

energy in the immediate vicinity, potentially resulting in erosion. Larger-scale 

effects, for example from removal of large or numerous structures in narrow 

parts of the estuary, seem unlikely but should be investigated before any such 

removal is undertaken.

ARTIFICIAL STRUCTURES

Available 

Habitat

Toxicity

Removal

3541 g. 6-3 articial structures

Desired

Species

Introduced

Species

Burial

Soft-bottom

Habitat

Sediment

Distributions

Current

Velocities

Spawning

Fishing

Access

Shade

Plant

Productivity

Attribute of physical structure

Threat to habitat

Function or species 

inuenced by the habitat

Inuence generally causing 

increase in target

Inuence generally causing a 

negative effect upon target

Factor causing either increase 

or decrease in target 

Figure 6-3: Influences on artificial structures, and functions and services provided by artificial 

structures. “Available habitat” refers to artificial structures that provide habitat for one or 

more species.
Chapter Six: Artificial Structures • 85

Many of the artificial structures in the bay have wooden pilings that were 

injected with creosote to minimize fouling (see Appendix 6-1). Creosote 

contains polycyclic aromatic hydrocarbons (PAHs) that are persistent in the 

environment and toxic to some organisms. Although the reproductive success 

of herring that spawn on creosote is unknown, experiments showed toxic 

effects on herring embryos from pieces of 40-year-old creosote-impregnated 

pilings (Vines et al. 2000). Strong circulation around pilings probably 

minimizes direct effects of creosote on motile organisms, but organisms that 

feed mainly on prey species inhabiting the pilings may be exposed to creosote 

through their food.

Piers and breakwaters, also often treated with creosote for its preservative 

qualities, are popular sites for recreational fishing because they provide 

easy access to the deeper waters of the bay and shoreline and because such 

structures attract fish.

Some other artificial structures may be local sources of toxic materials. For 

example, the reserve “mothball fleet” in Suisun Bay has released metals 

and paint debris into the estuary in the past; however, these ships are being 

removed, so such releases should not be a problem in the future.

The “mothball fleet” of ships from 

World War II has released heavy 

metals into Carquinez Strait.

This abandoned structure with 

creosote pilings presents both a 

human safety and environmental 

hazard.
86 • San Francisco Bay Subtidal Habitat Goals Report

Rock revetments (riprap) are one of the most abundant artificial substrates. 

Revetments lack the potential toxicity of pier pilings and may provide some 

of the same functions as natural rock substrate. However, before large-scale 

modification of the estuary, the areas now protected by rock would have 

consisted of mudflats and marshes, presumably more valuable habitat for 

supporting ecosystem services. Furthermore, the location and overall habitat 

value of constructed rock or concrete structures is unlikely to match that of 

natural rock, which often has a greater density and diversity of potential habitat 

for various organisms.

Rationale for Establishing Goals for Artificial Structures

Applying the approach outlined in Chapter 2 (Figure 2-1), it is clear that 

while artificial structures support some valued ecosystem services, they are 

not in short supply, and they can have some detrimental effects. If abandoned 

pier pilings interfere with the function of surrounding habitat, the decision 

tree would direct us to restore the surrounding habitat by removing the pier 

pilings. The advantages and disadvantages of doing this are being investigated 

and, if this activity is to be pursued, it should be done within an adaptive 

management framework (see Chapter 2) and based on recommended methods 

(see Appendix 6-1). Removing selected artificial substrates would be done in 

pilot projects to investigate and analyze the expected effects of eliminating 

this habitat and reversing its effects on local wave, current, and sedimentation 

patterns. One large-scale, long-term strategy for the Central Bay and the 

Richmond shoreline might be to restore eelgrass near sites where creosote 

pilings are being removed, to provide eelgrass as a natural substrate to attract 

spawning herring. 

Advantages of removal may include:

•	 Reduced substrate for introduced species

•	 Reduced shading of the bottom and water column

•	 Reduced toxic effects of creosote and other contaminants

•	 Reduced restrictions to flow and sediment movement 

•	 Restoration, re-creation, or realignment of intertidal mudflats, sand flats, 

rock, and shellfish, eelgrass, and macroalgal beds

Disadvantages may include:

•	 Disruption during removal (physical damage, turbidity, and toxicity)

•	 Reduced habitat for fish and invertebrates including native oysters

•	 Reduced resting or nesting sites for birds

Additional considerations for removal include:

•	 Reduced navigational hazards

•	 Aesthetics
Chapter Six: Artificial Structures • 87

•	 Reduced recreational fishing opportunities

•	 Loss of historical value and cultural connections

Goals for artificial structures focus on protecting the habitat value of existing 

and active structures, removing and preventing structures that are detrimental 

to the subtidal system, and improving our understanding of the role of artificial 

structures in the estuarine system. 

The recommendations that follow focus on the potential for removing 

derelict creosote pilings at pilot locations, and enhancing the subtidal 

functions that artificial structures offer (see Chapter 10 for more detail). 

Types of Artificial Structures

 in San Francisco Bay 

Ships and Vessels

• Recreational boats

• Commercial vessels

• Abandoned vessels

• Exposed shipwrecks (Point Molate)

• Sunken shipwrecks

• National Defense Reserve Fleet 

(Suisun Bay)

• Houseboats (Richardson Bay)

Pilings

• Marina areas

• Ports

• Vehicle bridges

• Foot bridges

• Fishing piers

Wharves

Floating Docks

• Private docks

• Public docks

Abandoned, Derelict Piers

• Berkeley Pier

• Point Molate Pier

Jetties

Breakwaters

• Riprap breakwaters

• Concrete breakwaters

Other Riprap

• Hardened shoreline functioning as 

levee

• Concrete blocks and other debris

Seawalls and Bulkheads

• Wooden seawalls

• Concrete seawalls

Buoys

Pipeline

Cables

Transmission Towers/Power Lines

Power Plants

• Cooling-water Intakes

Outfall Structures

• Power plants

• Water treatment plants

• Other pipelines

Duck Blinds

Moorings

Anchors

Pacific Oyster Shell 

(Restoration Projects)

Large Debris

• Shopping carts

• Tires

• Abandoned equipment

Derelict creosote piling structures 

on the North Richmond shoreline.
88 • San Francisco Bay Subtidal Habitat Goals Report

The recommendations incorporate information from the San Francisco 

Estuary Institute’s San Francisco Bay Creosote Piling and Artificial Structures 

Assessment (Appendix 6-1).

Science Goals for Artificial Structures

Artificial Structures Science Goal 1 

Understand how artificial structures generally affect the 

estuarine ecosystem.

Question A. How do pier pilings and other unused artificial structures affect wave 

and current patterns?

This question is general, concerned with the overall evaluation of the ecosystem 

services provided by these structures and the potential harm of either leaving 

them in place or removing them. 

Question B. What species use these structures for habitat, and is any of this 

use obligate?

Question C. How does habitat use change as areas of soft bottom and shoreline 

are converted to hard bottom, for example by construction of riprap?

Question D. How are rock-like artificial structures such as revetments and 

seawalls used by native oysters and other attached species, and how does that 

vary regionally?

These concrete “slagpools” provide 

limited habitat in comparison to a 

natural wetland or rocky intertidal edge, 

but can often show greater diversity 

of species and niche space than classic 

riprap. The pools host several species of 

seaweeds, mussels, oysters, barnacles, and 

a variety of other bay invertebrates.

Much of the bay shoreline has been riprapped.
Chapter Six: Artificial Structures • 89

The existing hard shoreline at Virginia Street on the Berkeley shoreline includes 

riprap, old concrete fill foundations from wharf and industrial facilities, and 

areas where concrete was simply poured onto the shoreline to act as a tidal 

barrier. 

Artificial Structures Science Goal 2 

Determine the roles of individual artificial structures proposed 

for removal.

Question A. What is the effect of removing a particular structure on local 

hydrodynamics and sediment transport?

This is related to Science Goal 1, Question A above, but concerns individual 

structures. The details of the structure, the physical configuration of the area, 

and the local current and wave environment all contribute to the alterations 

that a particular structure introduces. Removal may result in rapid erosion 

and resuspension of sediments when current speeds increase. Most of these 

structures fall below the spatial scale that today’s hydrodynamic models can 

resolve, so investigation may require developing small-scale models together 

with field studies.

Question B. Which species use this particular structure for habitat, and how?

Removal should be contingent upon an investigation into the habitat value of 

the particular structure in the environment where it is found.

Question C. How important is this structure for recreational use?

This question is related to the previous one but also to issues of access and 

current use. Some piers are heavily used for fishing, and other structures may 

be used for fishing or birdwatching because they attract fish or birds.

Children fish at the Marin Rod and Gun Club 

historic pier.
90 • San Francisco Bay Subtidal Habitat Goals Report

Protection Goals for Artificial Structures

Artificial Structures Protection Goal 1

Enhance and protect habitat functions and the historical value 

of artificial structures in San Francisco Bay.

•	 Artificial Structures Protection Objective 1-1: Improve water quality 

and hard substrate for habitat by encapsulating existing creosote pilings and 

piers, or by replacing them with inert materials, especially within current 

and historical herring spawning areas.

•	 Artificial Structures Protection Objective 1-2: When artificial 

structures (for example, shoreline stabilization structures) are installed, 

replaced, or maintained, use materials or methods that mimic natural 

habitat features, incorporate natural habitat (for example, emergent marsh, 

submerged aquatic vegetation, riparian vegetation, and oyster shell) into 

structure design, and use native seeding or other techniques to minimize 

establishment of invasive species. (See Chapter 10).

Artificial Structures Protection Goal 2 

Improve San Francisco Bay subtidal habitats by minimizing 

placement of artificial structures that are detrimental to 

subtidal habitat function. 

Please see Appendix 2-2 for more information on the impacts of artificial 

structures.

Restoration Goals for Artificial Structures 

Artificial Structures Restoration Goal 1 

Where feasible, remove artificial structures from San 

Francisco Bay that have negative or minimal beneficial habitat 

functions.

•	 Artificial Structures Restoration Objective 1-1: Where appropriate, 

remove creosote pilings from intertidal and subtidal habitats of the bay, 

with a focus on those areas that have high concentrations of individual 

pilings or piling complexes and are within current and historic spawning 

grounds for herring.

Artificial Structures Restoration Action 1-1-1: Initiate programmatic evaluation 

of pilings pursuant to the National Historic Register and associated 

guidelines.

Creosote Pilings

 in San Francisco Bay 

Wooden pilings have been 

used in marine construction 

projects for thousands of 

years. Beginning with the Gold 

Rush, wooden wharves and 

piers proliferated on the San 

Francisco waterfront. Several 

creosote plants operated in 

Alameda and other areas. The 

remnants of old creosotetreated piers and dilapidated 

maritime facilities are common 

sights along the intertidal and 

subtidal shorelines of San 

Francisco Bay. Creosote was 

used from the mid-1800s into 

the 1950s as a method for 

preserving marine structures 

from decay. It is a complex 

mixture of chemicals, many 

of which are toxic to fish 

and other marine organisms. 

Because of concerns over 

toxicity, creosote was banned 

in 1993 by the California 

Department of Fish Game.

Removal of these structures 

has been proposed as a 

possible restoration focus for 

San Francisco Bay. Creosotetreated wood and debris 

removal operations are 

underway in other regions 

of the United States. There 

is particular concern that 

chemicals leaching from 

creosote-treated structures 

could harm Pacific herring, 

one of the last fisheries in 

the region, because herring 

spawn on hard surfaces, 

including old pier pilings. 

There is also concern that 

dilapidated creosote-treated 

pilings are hazards to 

navigation and that they will 

pose even greater hazards 

as sea level rises. Removal 

and encapsulation projects 

conducted at the Port of 

Oakland and the Port of San 

Francisco are discussed in 

Appendix 6-1.
Chapter Six: Artificial Structures • 91

Artificial Structures Restoration Action 1-1-2: Remove 6,500 tons of creosote 

pilings from areas of high piling concentration (i.e., San Francisco 

Waterfront, Richmond Point, Napa River Mouth, and Carquinez Strait) 

within 5 years (see the following goal). 

•	 Artificial Structures Restoration Objective 1-2: Where appropriate, 

remove shoreline stabilization structures and riprap from the bay that are no 

longer providing protection or may be contributing to coastal erosion.

Artificial Structures Restoration Goal 2 

Promote pilot projects to remove artificial structures and 

creosote pilings at targeted sites in combination with a 

living shoreline restoration design that will use natural 

bioengineering techniques (such as native oyster reefs, stone 

sills, and eelgrass plantings) to replace lost habitat structure.

•	 Artificial Structures Restoration Objective 2-1: Fund three pilot 

restoration projects to test new material types and configurations for three 

types of artificial structures: riprap shoreline, breakwater, and dock. (See 

Chapter 10, Restoration Goals for Living Shorelines.)

There are more than 33,000 

derelict creosote pilings in San 

Francisco Bay.

 93

CHAPTER SEVEN

Shellfish Beds

This chapter addresses shellfish beds on hard substrate 

such as rock or shell aggregates, or mud/shell mix, together with 

the associated water column. (Shell hash areas in soft substrate are 

addressed in Chapter 4.) Shellfish beds are defined as locations where a 

shellfish species occupies more than 50% of an area of more than a few square 

meters (Schaeffer et al. 2007). Five species of shellfish occur in San Francisco 

Bay: native Olympia oysters (Ostrea lurida), California mussels (Mytilus 

californianus), hybridized Bay mussels (Mytilus trossulus/galloprovincialis), 

and non-native ribbed horsemussel (Geukensia demissa) and green bagmussel 

(Musculista senhousia). The latter two species are common in the estuary 

but do not occupy hard-bottom habitats and are not discussed further in 

this report. There are also small populations of the non-native Pacific oyster 

(Crassostrea gigas) in the South Bay, where eradication efforts are underway. 

Much of this discussion is based on Schaeffer et al. (2007), Grosholz et al. 

(2007), and Appendix 7-1.

Multiple age classes of native 

oysters can be found in rocky 

intertidal areas.
﻿94 • San Francisco Bay Subtidal Habitat Goals Report

Figure 7-1: Distribution of Shellfish Habitat in San Francisco Bay.
Chapter Seven: Shellfish Beds • 95

Of these species, the Olympia oyster is by far the most abundant and is the 

only species that is a native confined to estuaries. Recent surveys for oysters in 

the intertidal zone have found numerous individuals on hard substrates in the 

Central Bay and to a lesser extent in the San Pablo and South Bays (Figure 7-1; 

Zabin, et al. 2009). The abundance of oysters in the subtidal zone is unknown 

because methods for surveying them are inadequate. Oysters settle on natural 

soft substrate such as mud/shell mix (Chapter 4), hard substrate such as rock 

outcrops (Chapter 5), and some artificial structures (Chapter 6). 

Declines in extent of these rock habitats due to lowering for vessel traffic safety 

have been offset by the installation of artificial substrates (Chapter 6) such as 

riprap and seawalls.

Shells of native oysters occur in the vast shell middens at various sites around 

the bay along with those of mussels and clams, attesting to the pre-European 

settlement presence of the native oyster. However, the actual historical abundance of oysters is poorly known, in part because of confusion between native 

oysters and Ostrea lurida brought from Washington or Oregon and planted 

in the bay. Townsend (1893) referred to native oysters as very abundant and 

overgrowing the shells of eastern oysters which had been introduced for aquaculture. Commercial harvest was important “since the days of the Spaniards” 

(Bonnot 1935), and native oyster reportedly made up about 15% of the total 

oyster harvest from San Francisco Bay in the late 1800s to early 1900s, producing up to 150 tons of meat per year during 1888-1904 (Barrett 1963).

The vast majority of available information on native shellfish species is on 

native oysters, and most of the following discussion addresses native oyster 

beds. Many of these issues would also apply to other hard-bottom shellfish 

beds, although there may be less interest in restoring them at this time than 

there is for oyster beds. 

Various species of mussel can be abundant enough to form beds; most are 

confined to the more saline regions in and near the Central Bay where rocky 

substrates are common (Schaeffer et al. 2007). San Francisco Bay is marginal 

habitat for the native Mytilus californianus. The two native mussels (M. californianus and M. trossulus), and M. galloprovincialis, introduced in 1947, are 

common along the outer coast and presumably the bay populations are linked 

to the outer coast populations through larval exchange. The introduced Pacific 

oyster Crassostrea gigas may be completing its life cycle in the bay (C. Zabin, 

2009, pers. comm.).

ongoing Oyster restoration projects

Interest in restoring and maintaining oyster beds is demonstrated by the numerous

restoration and research projects underway in San Francisco Bay, Elkhorn Slough, and the

Pacific Northwest.

• http://www.bioone.org/toc/shre/28/1

• http://www.elkhornslough.org/research/conserv_oysters.htm

• http://www.habitat.noaa.gov/media/publications.html

The intertidal rocky shoreline is

covered in sea lettuce and native 

oysters.
﻿96 • San Francisco Bay Subtidal Habitat Goals Report

Conceptual Model for Shellfish Beds

Shellfish beds (Figures 7-1 and 7-2) provide several ecosystem functions and 

support several ecosystem services. The native oysters do not commonly 

form tall, three-dimensional reefs, as do Virginia oysters, although they can 

add structure to hard substrates and may be able to colonize and overgrow 

soft substrates. In this sense they can be considered a “foundation species” or 

ecosystem engineer, altering their environment by increasing bottom roughness, reducing current speeds, and as a result, trapping sediments. Oysters also 

increase physical heterogeneity, which can increase diversity of other marine 

invertebrates and also result in higher fish diversity and abundances than in 

neighboring, less complex habitats. Increased abundance of native oysters 

can locally increase the number of other benthic invertebrates (Kimbro and 

Grosholz 2006 for Tomales Bay). With their associated invertebrates, oysters 

provide food for fish, birds, and crabs. 

Not all the functions attributed to oyster beds are applicable in the San 

Francisco Estuary. One key function of bivalves in many estuaries and lakes 

is increasing water clarity. In locations such as the Chesapeake Bay, turbidity results mainly from high phytoplankton biomass, which can be severely 

Freshwater ow lowers

salinity, and sustained low

salinity can kill oysters.

 Dredging can damage beds

 and increase turbidity.

Adult oysters release larvae

which disperse in the water.

Oyster beds provide

habitat and food.

After several weeks, surviving 

larvae settle on hard substrate.

Dead oyster bed.

Turbidity limits the depth 

where oysters can grow. 

Mussels.

Wind waves,

 boat wakes,

 and currents

increase

 turbidity.

 

Other disturbances include 

boat anchorages, docks 

(shading), and contaminants.

Hg

Figure 7-2: Conceptual diagram for shellfish beds in the San Francisco Estuary.This diagram

displays processes that occur in and on shellfish beds,some of the ecosystem services these

habitats provide, and threats to shellfish beds.

A native oyster on cobble at the

Emeryville Crescent.
Chapter Seven: Shellfish Beds • 97

reduced by bivalve grazing. In the San Francisco Estuary most of the turbidity 

is due to inorganic particles (Kimmerer 2004). No effect on turbidity was noted 

after the invasion of the “overbite” clam, Corbula amurensis, in 1987, despite 

its enormous abundance in soft sediments of the brackish northern estuary 

(Alpine and Cloern 1992). Since the greatest conceivable extent of restored and 

natural oyster beds is minuscule compared to the area suitable for clams, it is 

unlikely that oyster beds could exert a measurable control on turbidity except 

possibly in water immediately over or near dense oyster beds.

So far very few oysters have been found on soft substrates, although that could 

be partly due to inadequate sampling, owing to the lack of suitable technologies to carry out broad-scale surveys in the shallow subtidal zone. Oysters in 

Puget Sound are able to colonize on soft substrates (Betsy Peabody, 2007 West 

Coast Native Oyster Meeting), but in San Francisco Bay oysters probably cannot establish beds on soft substrate without larger particles for attachment due 

to the high resuspension rates of soft sediments (due to shallow water and wind 

waves). Since oysters are known to settle on existing shell, oyster beds could 

become established on shell deposits if the deposits are not too mobile.

The time scale for dispersal of oyster larvae (~2 weeks) is shorter than estimates of residence time in the estuary, which are up to 60 days for the northern 

estuary in summer and much longer for the south bay (Walters et al. 1985). 

This implies that a large proportion of the larvae would settle within the estuary. However, within-bay currents are large enough to disperse particles among 

the major basins in a few days, implying that the propagules generally should 

disperse broadly within the estuary before settling. Apart from larval supply, 

several factors may limit the development and maintenance of oyster beds. 

Juvenile oysters are particularly vulnerable to poor environmental conditions 

and predation, so variation in mortality of juveniles presumably has a big 

effect on subsequent abundance. Food limitation is very likely given the low 

chlorophyll concentrations in the northern estuary (and formerly in the south; 

OYSTER BED

Destruction Establishment

Spawning Biological 

Diversity

Currents Substrate

Larval 

Supply

Sediment Predation

Inundation

Low 

Salinity

Acidification

Dredging

Boating,

Shipping

Attribute of physical structure

Threat to habitat

Other influence on habitat 

Function or species 

influenced by the habitat

Human-induced threat

Influence generally causing 

increase in target

Influence generally causing a 

negative effect upon target

Factor causing either increase 

or decrease in target 

3541 fig. 7-3 oyster bed

Available 

Habitat

Figure 7-3: Influences on oyster beds and their functions and services.

Native oysters colonize a mix of

hard and soft substrate at China

Camp State Park.
﻿98 • San Francisco Bay Subtidal Habitat Goals Report

Cloern et al. 2007). Food limitation generally results in low growth rate, which 

extends the time to maturity, decreasing survival of oysters to maturity. In locations with low larval supply from other beds, local larval settlement may be 

limited by the density of adult oysters in the bed. 

Threats to Native Oysters

The principal threats to native oysters seem to be high rates of sedimentation and extended periods of low salinity. Competition for space may be more 

important in the South Bay where hard substrate is limited and in the subtidal 

zone where fouling organisms such as sponges, tunicates, and hydroids are 

abundant. Intertidal substrate examined during surveys was around 40% clear 

of oysters, indicating that lack of attachment space may not limit abundance of 

intertidal oysters (Appendix 7-1). Other limiting factors include potential contaminant effects, especially for intertidal beds that are vulnerable to oil spills, 

and predation by fish, birds (for example, diving ducks), and possibly crabs. 

Oyster drills and small predatory snails present a low to moderate source of 

mortality to young oysters particularly in the South Bay. Diseases and parasites 

do not present a major threat, although this could change if population density 

increases and changes in water temperatures occur due to climate change. Heat 

stress in warm intertidal areas and overgrowth by algae may reduce oyster survival in local areas.

A recent bay-wide survey in 2006–07 (Appendix 7-1) found large areas of 

empty oyster shells in good condition, suggesting recent death. The high flows 

of 2006 may have reduced salinity for a long enough time in San Pablo Bay 

and possibly the South Bay to kill the oysters there. Daily mean salinity at the 

Romberg Tiburon Center monitoring site went as low as 5 ppm in spring of 

2006, and X2 (distance up the estuary to where tidally-averaged bottom salinity 

is 2 ppm, Jassby et al. 1995) went below 45 km for several days, and was below 

55 km for 3 months. This was the second longest duration of low salinity in 

the record since 1955 (Figure 7-4). Salinity in intertidal areas is subject to the 

large-scale salinity distribution in the estuary but can also be affected by local 

Below: Native oyster.

Bottom left: Native oysters settled

on rock.

Bottom right: Native oyster larvae

ready to disperse into the water

column.
Chapter Seven: Shellfish Beds • 99

runoff and discharge from wastewater treatment plants. This influence would 

be difficult to predict, and local runoff can be poorly correlated with flows 

through the delta. A San Rafael oyster restoration site lost around 99% of settled oysters after spring 2006, but the population recovered quickly (R. Abbott, 

Environ, 2009, pers. comm.).

Anthropogenic threats may include water pollution, boating, shipping, and 

dredging (Figure 7-5). If these activities occur near oyster beds they can 

directly disrupt beds or resuspend sediments that inundate beds. Ocean acidification is considered a growing threat to calcareous organisms in the ocean, and 

may become important particularly in the Central Bay with its strong oceanic 

influence. However, pH in much of the estuary may be controlled more by local 

processes (e.g., carbon dioxide input from sewage treatment plants and productivity cycles, Fuller 2010) than by any large-scale oceanic influence. 

3541 fig. 7-4 salinity frequency Cumulative Frequency

0

Days with X2 < 55 km

20 40 60 80 100 0

10

40

30

20

50

70

60

100

90

80

120 140 160

1956

1995

1983

1974 1982

1969

1967

1998 2006

1958

Number are years

Figure 7-4: Low-salinity events in San Francisco Bay.The graph shows the frequency distribution

of days with salinity less than 2 (near the landward limit of salinity penetration)

< 55 km, approximately at the Benicia Bridge.The mean return time for a low-salinity event

is the inverse of the frequency of events of at least that duration. For example, about 10% of

the years have had low-salinity events at least as long as that in 1982 (112 days),so such an

event can be expected roughly once in 10 years. Prediction of the frequencies of oyster die-offs

would be more precise given estimates of the salinity-time envelope for survival of oysters.

Data from Jassby et al. 1995 updated using the Interagency Ecological Program’s Dayflow data

(http://www.iep.ca.gov/dayflow/index.html).
﻿100 • San Francisco Bay Subtidal Habitat Goals Report

Figure 7-5: Locations of Shellfish Habitat Stressors in San Francisco Bay.
Chapter Seven: Shellfish Beds • 101

Rationale for Establishing Goals for Shellfish Beds

Shellfish beds are an intertidal to subtidal habitat created by the interaction 

of living organisms with particular physical conditions in the estuary. Several 

functions of shellfish and specifically oyster beds discussed above could be considered helpful in moving the estuary toward a more natural, less uniform state 

with local heterogeneity benefiting some species. In regards to restoration, it 

remains to be seen whether it is possible to establish persistent oyster beds over 

a large enough area to have substantial ecological impacts. However, smallscale restoration projects have reported increases in species use such as herring 

depositing roe on the structures and birds feeding on them (R. Abbott, 2009, 

pers comm.). It may be prudent to continue to research methods to establish 

oyster beds, while also further investigating their ecosystem functions. It is also 

not clear to what extent the functions of restored oyster beds are due to the 

oysters or to the structures put in place to allow oysters to settle. 

Applying the approach outlined in Chapter 2, it is clear that the restricted 

extent of oyster beds may be limiting their support of valued ecosystem services. Furthermore, restoration has been demonstrated and is therefore feasible 

(Appendix 7-1), although questions remain about the anticipated trajectory 

of restoration and associated response of ecosystem functions and services. 

Therefore, restoration is warranted for oyster beds, but should be done within 

an experimental framework (see Adaptive, Phased Approach below and discussion of adaptive management in Chapter 2).

Ongoing restoration work near San Rafael has succeeded in obtaining population growth and good recruitment in at least some years. The oysters grow well, 

reach reproductive capacity early, are free of disease and parasites, and have 

low losses to predation (R. Abbott and C. Zabin, 2009, pers. comm.). Providing 

a substrate with highly complex surface areas (bagged clean Pacific oyster 

shells) results in high rates of settlement and abundant oysters, compared to 

less complex substrates such as riprap. Required maintenance appears to be 

minimal (R. Abbott, 2009, pers. comm.). 

If restoration (including enhancement or creation) of oyster habitat should 

proceed, many aspects of the process will require investigation and refinement. 

Restoration projects should move towards larger-scaled pilot projects, but the 

focus should be on the value of knowledge gained as well as the value of the 

restoration projects themselves. Experimental restoration will help to answer 

At right: Mobile oyster larvae

swimming in the water column.

Far right: Native oysters settled on

Pacific oyster shell.

Below: Size difference between

small native oysters and large 

Pacific oyster shell, used as a

substrate for oyster restoration.

Bottom: Monitoring plate with

newly settled oysters, tunicates, and

barnacles.
﻿102 • San Francisco Bay Subtidal Habitat Goals Report

broader-scale questions about the likely outcomes of restoration. Regardless 

of the extent of future restoration, oyster beds remain potentially valuable 

resources. The success of restoration, protection, and management depends on 

adequate understanding of how these beds develop, how they are maintained, 

and what threats they face.

The beds formed by mussels do not appear to be a priority for restoration in 

San Francisco Bay, because the beds are small, little is known of their ecological 

importance, and the mussels are abundant on the open coast and in other estuaries. There may be interest in researching the interaction and hybridization of 

Mytilus galloprovincialis with the native M. trossulus, but managing them would 

be difficult since these species and their hybrids are not easily distinguished.

Goals for shellfish bed habitat focus on protecting existing native oyster beds, 

creating and enhancing additional beds, and improving our understanding 

of ecosystem services, factors influencing the beds, and restoration methods, 

in order to improve our ability to protect and restore this habitat. The principal restoration goal, pending a satisfactory determination of its benefit, is to 

restore large areas of habitat suitable for native oysters. The 50-year maximum 

restoration targets are based on the acreage of shoreline areas out to a depth 

of 2m where native oysters have been documented, and correlate with recent 

monitoring data regarding distribution. Native oysters would not be restored 

throughout these target areas, but at a subset of locations within these larger 

Biologists install bagged Pacific

oyster shell reefs at the Marin Rod

and Gun Club restoration site in

San Rafael.

Mounds of Pacific oyster shells

and eelgrass “seed buoys” (see

stakes in the background) were used

to restore oysters and eelgrass at 

the Marin Rod and Gun Club.
Chapter Seven: Shellfish Beds • 103

areas. The long-term acreage targets were developed with the assumption that 

without restoration efforts native oyster abundance will remain relatively stable. 

Should native oyster acreage increase considerably independent of restoration 

efforts, that increase should count towards the overall acreage target.

An Adaptive, Phased Approach to Oyster Restoration

An adaptive approach to restoration, conducted in phases from small scale 

to large (Appendix 7-1), would have two key advantages. First, the effort can 

begin at small enough scales to be tractable and to allow for the learning necessary to expand the scale of restoration projects in subsequent phases. Second, 

within a program of adaptive management, pursuing restoration in phases can 

ensure that information is gathered to answer the fundamental questions about 

the roles of oyster beds (i.e., questions under Science Goal 1, below) and the 

responses of oyster beds to environment (Science Goal 2), as well as questions 

related to restoration itself (Science Goal 3). That is, at each phase, investigations into the roles and responses of oyster beds and the relationship of these 

to the scale of the restoration will be embedded in any significant restoration 

project.

The phased approach begins with selecting sites for experimental restoration 

projects, mainly to refine site selection and restoration methods. Results from 

this phase will be used to design the pilot phase, which will scale methods to 

larger areas and also begin to gather evidence on the likely outcomes of restoration. Depending on results from the pilot phase, restoration could then be 

attempted at larger sites, with each step contingent on the development of evidence in previous phases indicating a high value for restored oyster beds.

The knowledge developed during each phase will be critical for answering 

the key research questions enumerated below. These include determining the 

effectiveness of oyster restoration in providing valued ecosystem services, the 

environmental controls on oyster beds, and the methods that will maximize the 

success of the restoration. Of these questions, the most critical is the provision 

of ecosystem services, since this is the justification for attempting restoration 

beyond the experimental scale. Thus, understanding of the extent of ecosystem 

services provided by restored oyster beds should be improved substantially at 

each phase beginning with the pilot phase, before the process moves into the 

next phase. To continue restoration without this knowledge could risk wasting 

public money if the restoration proves ineffective, and could jeopardize support 

for these and other restoration activities.

Before restoration is undertaken, principles for site selection should be established. These could include local conditions (for example, depth profile, sediment type, waves and currents, salinity patterns, turbidity) and the environmental context (for example, proximity to hardened shorelines, ports or piers, 

proximity to source beds for larvae, convenience for access and monitoring), 

taking into account likely changes in these attributes with long-term trends 
﻿104 • San Francisco Bay Subtidal Habitat Goals Report

such as sea level rise and increasing water clarity. Initial work has been completed (Appendix 2-2 and 7-1).

Restoration phases may overlap to some extent; for example, evaluation could 

begin as soon as a year or more of data were available from each project. To 

maximize knowledge gained from each project, basic monitoring (for example, 

abundance of oysters) should continue annually after the end of the project; 

thus each project should be funded for a long enough period to encompass the 

design, construction, operation and monitoring, reporting, and post-project 

monitoring. The decision to terminate this monitoring should be based on the 

knowledge foregone by termination as well as by the additional cost of ongoing 

monitoring. Monitoring of the large-scale restoration projects should continue 

indefinitely to allow for answers to be developed about the long-term trajectories and responses to environmental conditions.

Native Oyster Monitoring and Restoration Pilot Projects

• Holly Harris, San Francisco State University: 1999 monitoring study, 2004 Masters Thesis

• Save The Bay/ San Francisco State University: 2001–02 recruitment study

• Richardson Bay Audubon Center: 2004–2010 monitoring and recruitment studies

• Marin Rod and Gun Club, Robert Abbott, Rena Obernolte, et al:

2004–2010 restoration project

• Berkeley Marina, Robert Abbott, Rena Obernolte, et al: 2010 restoration project

• Outer Bair Island, Robert Abbott, Rena Obernolte, et al: 2004–2006 recruitment study

• Pt Pinole Pier area, Obernolte et al,TheWatershed Project: 2006–2010 recruitment study

• Save The Bay/San Jose State University: 2006–2007 recruitment study

• UC Davis, Zabin, Grosholz et al: 2007–2010 monitoring and recruitment studies

Above left: Marin Conservation Corps members and community volunteers bag Pacific oyster

shell for restoration. Above right:A Marin Rod and Gun Club member shows a Pacific oyster

shell string, another method of monitoring oyster recruitment.
Chapter Seven: Shellfish Beds • 105

Phases in an Oyster Restoration Effort

Phase I. Experimental restoration

This phase will develop the experimental design for the

restoration to answer key questions about sites and methods

(science goals).The phases within this group should be

followed in sequence but can be accomplished for different

sites at different times.

Phase I-1: No prior knowledge of site

Conduct a basic site survey.

Phase I-2: Limited site knowledge

Condition: Mapping or surveys have been conducted.

• Assess suitability of the site for restoration.

Phase I-3: Experimental restoration

Condition: Phase 1-1 and 1-2 actions completed; area is unlikely

to recruit naturally and is suitable.

• Determine experimental design to fit the site.

• Establish replicated small-scale test plots at various

elevations, and other treatments.

• Evaluate outcomes: persistence,recruitment, abiotic

conditions, use by other organisms.

• Report evaluates restoration potential and lessons learned.

Following this phase an evaluation takes place in which

decisions are made about whether and to what extent

to proceed into pilot restoration. This decision should be

made largely on the basis of feasibility and conditions at

individual sites.

Phase II: Pilot restoration

This phase will expand on the previous experimental phase to

determine the suitability of alternative methods of restoration

at a larger scale than the experimental scale. It will also begin

to evaluate the larger implications of restoration for its value

in increasing the provision of ecosystem services (science

goals 1 and 2 below).

Condition: Phase I has been completed for candidate site, and

site remains suitable.

• Design small pilot restoration project (0.5 acre or less) to

test hypotheses developed or provisionally tested in Phase I.

• Design includes explicit measures to determine

quantitatively the use of the restored site by organisms

and other evidence about the likely benefits of restoration.

• Establish replicated moderate-scale test plots.

• In the second year of the program, begin to assess aspects

of ecosystem function (e.g.,spawning substrate and

nursery and foraging habitat).

• Evaluate outcomes including those in Phase I, and aspects

of ecosystem function.

• Report findings including evaluation of restoration

potential, value, and lessons learned.

Following this phase an evaluation takes place in which

decisions are made about whether and to what extent to

proceed into larger-scale restoration.The decision about

whether to expand the scale of restoration should be

based on an assessment that the restored oyster beds

likely provide ecosystem services commensurate with the

cost and effort involved in the restoration.This decision

could be made provisionally on the basis of a few pilot

projects, and re-evaluated as more pilot projects are

completed.The decisions about where and how to restore

should be based on lessons learned from individual sites

about feasibility and conditions.

Phase III. Larger-scale restoration project

This phase will expand on the pilot phase with the

principal purpose being to evaluate the larger implications

of restoration for its value in increasing the provision of

ecosystem services (science goals 1 and 2 below).This phase

will also determine how alternative methods of restoration

scale up beyond the pilot scale.

Condition: Phase II has been completed for candidate site, and

site remains suitable.

• Design intermediate-scale restoration project (~1 acre)

to answer questions under science goals 1 and 2, and to

further develop the art and science of oyster restoration.

• Design includes explicit measures to determine

quantitatively the use of the restored site by organisms

and other evidence about the likely benefits of restoration.

• Establish replicated larger-scale test plots.

• In the second year of the program, begin to assess aspects

of ecosystem function (e.g.,spawning substrate and

nursery and foraging habitat).

• Evaluate the response of ecosystem functions and likely

ecosystem services.

• Report findings including evaluation of restoration

potential, value, and lessons learned.

If the value of the restoration as estimated in this phase

continues to suggest further expansion, this phase may

be repeated at different sites as pilot programs are 

completed, and the acreage target expanded at each

site and the above process repeated.The decision about

whether to expand the scale of restoration should be

based on an assessment that the restored oyster beds

likely provide ecosystem services commensurate with the

cost and effort involved in the restoration.This decision

would remain provisional with additional information

coming in as pilot and then larger-scale projects are

completed.The decisions about where and how to restore

should be based on lessons learned from individual sites

about feasibility and conditions.

At this scale a critical issue is the long-term viability of the

restored oyster beds and their provision of ecosystem

services.
﻿106 • San Francisco Bay Subtidal Habitat Goals Report

Science Goals for Shellfish Beds

Shellfish beds Science Goal 1

Understand the ecosystem services the shellfish beds support, 

and in what quantities, in their current state and after restoration. 

Question A. What specific functions do shellfish beds support?

This question could be addressed in part by an examination of extant beds in 

different parts of the bay, supplemented by lessons learned during early restoration. These lessons may be transferable among sites if the influence of local 

conditions can be understood and quantified.

Question B. How much is attributable to the structure vs. the shellfish? 

The basis for this question is discussed above. 

Question C. How do the ecosystem services provided by restored oyster beds scale 

with the total area restored and its spatial configuration?

If oyster beds are being restored to support ecosystem services, enough beds 

must be restored to provide a substantial increase in these services. These services may scale linearly with the increase in bed area, or some other way (see 

discussion of restoration and ecosystem services in Chapter 3). The shape of 

this relationship presumably depends on feedbacks between the existing bed 

structure and both settlement success and mortality. This would be difficult to 

determine, particularly before restoration began. Assuming a 

linear response, though, it should be possible to calculate the 

extent or value of an ecosystem service of constructed oyster 

reefs, perhaps in terms of food, structural habitat for fishes 

and birds of concern, and shoreline protection per unit area or 

shoreline distance. This information could be used to project 

the value of the restored habitat, and this projection could be 

periodically updated with newly gathered data.

A corollary of this question is how the degree of fragmentation 

of the habitat influences its function, i.e., whether a series of 

fragments performs the same function as a contiguous habitat 

of the same area.

Question D. What is the current extent of subtidal populations 

of oysters?

Intertidal oyster beds have been partially inventoried, but 

subtidal oyster beds are hard to see and most remote-sensing 

techniques are unsuited for use in shallow water. Knowing the 

extent of these beds is essential for answering the other questions about oyster beds, including their ecosystem-level effect 

and the large-scale impacts of restoration.

Native oysters are established on

rock and soft substrates near Rat

Rock in China Camp State Park.
Chapter Seven: Shellfish Beds • 107

Shellfish BEDS Science Goal 2

Understand the factors controlling the development and persistence of oyster and other shellfish beds.

Question A. How do individual beds respond to their local biotic and abiotic 

environment?

Salinity, temperature, wind and wave patterns, currents, sediment delivery, and predation or consumption may all play a role in the growth or 

shrinkage of oyster beds. However, these influences are understood only 

at the most basic level. The relationship between initial settlement of oyster larvae and hydrodynamic conditions, and between survival and both 

hydrodynamics and sediment supply, may determine population growth. 

However, predators can play an important role. Since oysters on a reef 

can be inventoried and examined, it should be possible to determine 

their population dynamics and mortality factors.

Question B. What limits the establishment of new beds, either under natural conditions or as restoration projects?

Oysters in the intertidal zone occupy less than half of the available space 

in regions where they occur. The extent of settlement may be related to 

larval supply, provided the available space is actually suitable for settlement. However, other unknown factors may be limiting the establishment of new beds.

Question C. How does estuarine circulation influence the movement of larvae 

and subsequent recruitment?

Once beds have been established, the potential exists for them to send larvae to 

other areas of the estuary and to establish remote daughter beds. This potential 

depends on duration of the larval stage and the very specific details of circulation both at the scale of the beds themselves and at a broader scale. Large restoration sites may contribute to settlement and even establishment of beds in 

remote locations provided the substrate is available and the local and regional 

currents are favorable. At the scale of individual beds, the rate of settlement is 

likely affected by local conditions and the behavior of late larval stages as well 

as the rate of supply of larvae.

Question D. What is the degree of connectivity among beds?

The previous question can be turned around: how do population and genetic 

structure vary among beds, and what can that tell us about the connectivity 

among beds? This is a particularly important component for understanding the 

larger-scale issues raised under Science Goal 1. Note that genetic structure and 

ecologically relevant population structure are likely to be different and operate 

at different scales, and require different tools for investigation. Research to date 

indicates some genetic structure among oyster beds (Jim Moore, 2008, CDFG, 

pers. comm.).

Dense beds of native oysters

provide multiple habitat benefits,

including establishing on available

space and outcompeting non-native

invasive species.
﻿108 • San Francisco Bay Subtidal Habitat Goals Report

Question E. What influences survival of newly settled oysters?

Juvenile oysters are more vulnerable than adults to predation and other causes 

of mortality, and therefore variation in juvenile mortality can have a big effect 

on subsequent abundance.

Question F. What is the extent of mortality in oyster beds due to exogenous factors and how fast do the beds recover?

Low salinity caused die-backs on restored oyster beds in 2006, although the 

oyster populations on these beds rebounded quickly. Other potential hazards to 

oyster beds include oil spills, contaminant inputs, and physical disturbance. 

Shellfish BEDS Science Goal 3

Develop the most effective ways of restoring and protecting 

oyster beds. 

Question A. How do physical structures, materials, spacing, and orientation of 

restored beds interact with the local environment to influence settlement and 

survival?

Local conditions including salinity, currents, and the supply rate of food, sediment, and larvae are likely to influence settlement and survival. Design and 

construction of oyster beds may influence settlement and survival differently 

depending on these local conditions. Therefore lessons from one site may not 

be entirely transferable to another. 

Question B. What is the influence of predation, parasitism, disease, and algal 

overgrowth on the success of restoration?

Parasitism and disease have not yet been identified as significant factors in 

the dynamics of oyster populations in the estuary. This could change with 

increasing population density, and effects are likely to be sporadic and therefore difficult to detect and assess. Consumption by predators is both a source 

Below left:Volunteers make Reef

BallsTM, artificial reef structures

composed of native bay sediments 

(mud and sand), historic dredged

oyster shell, and a small amount of

Portland cement.

Below right: Volunteers retrieve

shell bags from constructed reefs

to monitor them onshore.
Chapter Seven: Shellfish Beds • 109

of mortality and a means by which the beds support ecosystem processes, so 

some amount of consumption is consistent with “success.” Algal overgrowth 

has been identified in some beds.

Question C. How can beds be designed and built so as to make them selfsustaining and minimize the need for ongoing intervention?

Oysters must be dense enough on the beds to allow for reproduction. The 

minimum density probably depends on the physical layout and local currents. 

Ongoing restoration efforts indicate that oyster beds need to be cleaned of 

sediment periodically but require no other maintenance. Minimizing human 

intervention would reduce the cost of restoration and increase the likelihood of 

long-term persistence of the beds. This of course does not eliminate the need 

for periodic monitoring.

Question D. How do oyster beds and eelgrass beds interact, and how do they 

interact with other habitats?

Since some of the functions of eelgrass and oyster beds are similar, there may 

be advantages to establishing them in close proximity. Also, restoration should 

take into account potential negative effects on other habitats or services.

Question E. What are the best methods and timing for oyster restoration that 

minimize settlement of invasive species?

Question F. How do wind waves, wakes, water intakes, and turbidity affect 

oyster beds?

Wave action can affect beds directly or indirectly through increases in turbidity 

and suspended sediment. The degree and spatial extent of disruption to oyster 

beds by vessel wakes and turbidity and suspended sediment from wakes or 

dredging should be investigated to determine if protective actions are needed. 

Industrial intakes of water might entrain an excessive proportion of larvae if 

the intakes are located close to large oyster beds or restoration sites.

Volunteers monitor individual

Pacific oyster shells covered in

newly settled native oysters.
﻿110 • San Francisco Bay Subtidal Habitat Goals Report

Question G. How do constructed oyster beds influence local water motion and 

sediment deposition?

Potential positive and negative effects of the beds as structure must be considered in designing and building oyster beds. These may affect the long-term success of the beds as well as conditions in the surrounding areas.

Protection Goals for Shellfish Beds

Shellfish Beds Protection Goal 1

Protect San Francisco Bay native shellfish habitats (particularly native oyster Ostrea lurida) through no net loss of 

existing habitat. 

•	 Shellfish Beds Protection Objective 1-1: Provide public access and 

recreational opportunities that minimize impacts to existing intertidal native 

shellfish habitat in the bay.

Shellfish Beds Protection Action 1-1-1: Develop community stewardship of 

native shellfish beds through placement of educational materials and signs 

that educate the public about the importance of shellfish bed habitat. Place 

educational signs at high-density intertidal sites and at restaurants serving 

oysters, and work with agencies to include shellfish information in Water 

Trail, Bay Trail, and Department of Boating and Waterway educational 

materials. 

•	 Shellfish Beds Protection Objective 1-2: Support preservation of 

existing intertidal and subtidal native shellfish habitat by locating new or 

reconstructed structures and shoreline infrastructure, or new dredging 

projects, away from high density native shellfish beds.

Shellfish Beds Protection Action 1-2-1: When new construction or operation 

of shoreline infrastructure occurs close to shellfish habitat, conduct preconstruction surveys of native shellfish to determine if significant populations (high densities, large adults, multiple age classes) are present.

Native oysters colonized on

rocky substrate or possibly on 

artificial substrate such as a

discarded tire.
Chapter Seven: Shellfish Beds • 111

Shellfish Beds Protection Action 1-2-2: Promote partnerships with cities and 

counties to ensure that all proposed water intakes (for example, from oncethrough cooling and desalination facilities) minimize impacts to native 

shellfish beds by locating structures away from existing native shellfish beds 

and promoting use of technologies that avoid high levels of larval entrainment (for example, subsurface intakes near large shellfish beds). 

Shellfish Beds Protection Goal 2

Protect areas in San Francisco Bay with potential for future 

shellfish expansion, restoration, or creation.

•	 Shellfish Beds Protection Objective 2-1: Purchase subtidal property 

from willing sellers or create conservation easements for shellfish protection 

or restoration (including enhancement or creation). (Potential sources 

of funding may include the National Fish and Wildlife Foundation, The 

Nature Conservancy, State Coastal Conservancy, Audubon, NOAA Coastal 

Estuarine Land Conservation Program, land trusts, etc.). 

•	 Shellfish Beds Protection Objective 2-2: If new projects are located in 

intertidal or subtidal areas, scale and orient them in ways that maintain or 

improve physical conditions (bathymetry, currents, etc.) needed to support 

shellfish survival and growth in areas identified in this report for future 

native shellfish habitat enhancement or creation projects.

Native oysters and seaweeds attach

themselves to monitoring stakes as

part of a project by San Francisco

State University researchers on the

North Richmond Shoreline.
﻿112 • San Francisco Bay Subtidal Habitat Goals Report

Restoration Goals for Shellfish Beds

Shellfish Beds Restoration Goal 1

Increase native oyster populations in San Francisco Bay within 

8,000 acres of potential suitable subtidal area over a 50-year 

time frame through a phased approach conducted within a 

framework of adaptive management.

•	 Shellfish Beds Restoration Objective 1-1: Implement a program of 

adaptive management with phased restoration. Periodic reviews will 

determine whether the knowledge is adequate to support proceeding to 

the next phase. Provisionally the targets would be to increase native oyster 

populations within 10 acres of subtidal area within 5 years, within 400 acres 

of subtidal area within 10 years, and within 8,000 acres of subtidal area 

within a 50-year time frame (Figure 7-6). 

•	 See list of priority native oyster restoration sites below, and more detail 

in the Native Oyster Restoration Table in Appendix 7-1 for site-specific 

phased actions. 

Recommendations for Restoring Oyster Beds

In areas with potential for restoration, UC Davis researchers estimate total potential

acreage at preferred sites as 8,000 acres, the area defined by the shoreline segment

out to 2m depth, which is about 9% of the total intertidal and subtidal habitat from the

shoreline to a 2m depth.The site recommendations below are based largely on the

recommendations from previous monitoring and restoration projects, twoWest Coast

Native Oyster workshops, and the San Francisco Bay Native OysterWorking Group,

and from participants in a workshop on shellfish restoration held in Tiburon, California

in December 2008.

Priority native oyster restoration sites:

Earl F. Dunphy Park, Sausalito

Brickyard Park, Strawberry

Angel Island

Richardson Bay

Arambaru Island, Richardson Bay

San Rafael Shoreline from Marin Rod

& Gun Club to south of McNears

Beach area

Marin Islands NationalWildlife Refuge

Richmond Bridge north to Point

Pinole

Point Isabel Regional Shoreline

Albany Beach

Berkeley Shorebird Park

Ashby Spit to Emeryville Crescent

North Cesar Chavez Park, Berkeley

Lake Merritt, Oakland

Oakland Middle Harbor

Area adjacent to San Leandro Marina

and nearby shoreline

Eden Landing Ecological Reserve,

Hayward

Ravenswood Pier

South Bay Salt Ponds and adjacent

offshore subtidal areas

Palo Alto Baylands Nature Preserve

West Point Harbor, Redwood City

Bair Island NationalWildlife Refuge,

Redwood City

Coyote Point, San Mateo

Oyster Point to area adjacent to

Sierra Point Marina, South San

Francisco
Chapter Seven: Shellfish Beds • 113

Figure 7-6: Locations of recommended sites for phased native oyster restoration in San

Francisco Bay.
﻿114 • San Francisco Bay Subtidal Habitat Goals Report

Shellfish Beds Restoration Action 1-1-1: Establish a standing objective review 

panel to evaluate results and make recommendations on stepping through 

phases of restoration.

Shellfish Beds Restoration Action 1-1-2: Develop an integrated program of 

research, pilot projects, and eventually full-scale projects following the adaptive management framework (Chapter 2, Figure 2-3, see Phased Approach 

above), with the intent of simultaneously increasing the area of shellfish beds 

and learning about their contributions to ecosystem services. Specific attention should be paid to assessing the quantitative ecosystem response to restoration, and the resulting increases in ecosystem services to be expected.

Shellfish Beds Restoration Action 1-1-3: Develop a programmatic environmental review and permitting process to facilitate subtidal restoration projects, 

including native oyster restoration projects, to achieve multiple habitat and 

shoreline protection objectives. 

•	 Shellfish Beds Restoration Objective 1-2: Incorporate native oyster 

restoration into other regional restoration and shoreline protection projects 

and initiatives. 

Shellfish Beds Restoration Action 1-2-1: Initiate pilot subtidal integration projects, including living shorelines and living breakwaters, to demonstrate 

effectiveness and collaboration. When appropriate, construct living shorelines, including reef ballsTM and other techniques, from native, biodegradable 

materials, maintenance dredging material that can be beneficially reused, or 

native rock.

Shellfish Beds Restoration Action 1-2-2: Support public–private partnerships 

to restore native oysters. Work with regional organizations and agencies to 

identify partners and projects that could incorporate native oyster restoration and monitoring into existing or planned projects. Groups include the San 

Francisco Bay Joint Venture, California Department of Fish and Game, Jerico 

Products, Inc., the Wildlife Conservation Board, and others.

Shellfish Beds Restoration Action 1-2-3: Incorporate San Francisco Bay oyster 

restoration goals into national strategies such as The Nature Conservancy 

Shellfish at Risk Program and the National Fish and Wildlife Foundation’s 

Keystone Species Initiatives.
 115

Chapter Eight

Submerged Aquatic Vegetation

The term “submerged aquatic vegetation” (SAV) refers to 

all underwater flowering plants. In the San Francisco Estuary, SAV 

includes sago pondweed (Stuckenia pectinata, formerly Potamogeton 

pectinatus), eelgrass (Zostera marina), and other species of seagrass, including 

the surfgrasses (Phyllospadix torreyi and P. scouleri), and widgeongrass (Ruppia 

maritima) (Schaeffer et al. 2007). Several freshwater plant species, mostly 

introduced, are found mainly in the delta (for example the Brazilian waterweed 

Egeria densa, an invasive nuisance species) and are outside of the geographic 

scope of this project.

This chapter focuses almost exclusively on eelgrass. In San Francisco Bay, 

eelgrass is much more extensive than other SAV, and its role and restoration 

potential are understood better than for other SAV (Appendix 8-1). No quantitative information is available on the extent of eelgrass in the estuary before 

the 1980s. Because the estuary’s water is so turbid, eelgrass was long believed 

An eelgrass bed at Keil Cove on the Tiburon Peninsula.
﻿116 • San Francisco Bay Subtidal Habitat Goals Report

to be uncommon. However, a survey in 1987 reported 128 hectares (316 acres) 

of eelgrass, determined by inspection and depth-sounding from small boats 

(Wyllie-Echeverria and Rutten 1989). Surveys using side-scan sonar in 2003 

and 2009 found 1,166 and 1,500 hectares of eelgrass beds, respectively (or 

2,900 and 3,700 acres respectively), in the subtidal regions of the estuary 

(Merkel 2004, 2010; see Figure 8-1). However, Merkel (2004) reported that 

most beds identified from the 1987 survey were larger in the 2004 survey. The 

more recently determined areas of eelgrass comprise about 1% of the total 

estuarine area of around 120,000 hectares (or 300,000 acres at mean sea level), 

not including the delta. 

Several factors could have contributed to an increase in eelgrass extent 

between 1987 and 2003–2009. These include a decrease in suspended sediment in the estuary that occurred around the end of 1998 (Schoellhamer 2009), 

the long-term improvement in water quality in the bay since the passage of 

the Clean Water Act, and effects of the 1983 flood and resulting months-long 

depression of salinity throughout the bay. The increase in reported coverage 

since 1987 is at least partly due to the much more efficient techniques used in 

the later surveys. 

The reported increase in total acreage from 2003 to 2009 should not be taken 

as firm evidence of a trend until more surveys have been completed, as all 

biological populations undergo interannual variation. Furthermore, detailed 

surveys of individual beds have shown interannual variability in the extent and 

density of these beds as well as in their reproductive mode, and genetic studies have shown variability among beds, indicating some reproductive isolation 

(Appendix 8-1). Thus, not only is there interannual variation, but different beds 

of distinct genetic makeup could vary in different ways.

The largest eelgrass beds in the estuary are in the shallow subtidal regions of 

San Pablo Bay and Richardson Bay, with smaller beds scattered in shallow areas 

mainly between Carquinez Strait and the Eden Landing Ecological Reserve in 

Hayward (see Figure 8-1). The largest bed in the bay is located between Point 

San Pablo and Point Pinole on the East Bay shoreline, and comprises about half 

of the total acreage.

The maximum potential coverage of eelgrass is predicted to be 9,490 hectares 

(23,440 acres) (Merkel 2005), or about 9% of the bay, as determined by a habitat suitability model based on bathymetry (probably accurate only in water 

accessible by boat), current speed, exposure to wind waves, residence time, 

and the locations of extant eelgrass beds. Habitat characterized by the model 

as suitable for the establishment of eelgrass beds occurs at depths less than 

about 2 m in broad swaths along the shores of San Pablo, Central, and South 

Bays. About half of this acreage was classified as moderately suitable (modeled 

habitat suitability index of 34–66%) to highly suitable (67–100%). To date, restoration attempts within areas of high predicted suitability have been successful (Appendix 8-1). An area of Richardson Bay predicted by the model to have 
Chapter Eight: Submerged AquaticVegetation • 117

Figure 8-1: Distribution of Submerged AquaticVegetation Habitat in

San Francisco Bay. Locations for sago pondweed and widgeon grass are approximate.
﻿118 • San Francisco Bay Subtidal Habitat Goals Report

low suitability (0–33% range) did not support development of an eelgrass bed 

during a seeding experiment (Boyer et al. 2008).

Bay-wide surveys of eelgrass distribution were conducted in 1987, 2003, and 

2009. A more detailed study was conducted in 2006–2009 of seven eelgrass 

beds chosen to represent a range of conditions and the geographic extent of 

eelgrass beds in the Bay (see Figure 8-2). Researchers visited the seven beds in 

spring and summer of each year. Results to date show considerable variability 

in shoot density among beds, and changes in bed characteristics seasonally and 

interannually (Appendix 8-1). 

Conceptual Model for SAV

Seagrasses perform a wide variety of functions (Figures 8-3 and 8-4; Phillips 

1984, Orth et al. 2006, Waycott et al. 2009). They alter local hydrodynamics, 

reducing the speed of currents. In doing so, they trap and stabilize fine sediment, reducing the average grain size in the bottom sediments and altering the 

local sediment chemistry. Globally they are much more productive per unit 

area than phytoplankton (Duarte and Chiscano 1999). Eelgrass transforms 

unstructured shallow-water areas into physically structured habitat that can 

support a wide variety of organisms. The complexity of this habitat can support residents that have a variety of life histories and feeding modes (Robertson 

1980). Eelgrass beds have higher abundance, biomass, and productivity of consumer organisms than do unstructured habitats (e.g., Connolly 1997). Seagrass 

beds also provide a food source, either directly to grazers on the seagrass 

(amphipods, snails, ducks, geese) or indirectly, either to grazers on epiphytes, 

i.e., plants such as diatoms growing on grass blades, or predators consuming 

invertebrate grazers, or through detritus formed of dead plant material that 

supports the estuarine food web. Few fish species consume seagrasses directly, 

so the food supply from the seagrass beds to fish is indirect. Finally, seagrass 

beds can serve as ecological sentinels, providing advance warning of deteriorating conditions such as increasing turbidity, wave action, temperature, or contaminants (Orth et al. 2006).

Eelgrass beds thrive in Richardson Bay and Raccoon Strait.
Chapter Eight: Submerged AquaticVegetation • 119

Figure 8-2: Locations of San Francisco State University’s Seven Site Eelgrass Bed Survey

(2005–2010).

Pt. San Pablo

Pt. Molate

Keller Beach

Richardson

Bay

Angel Island

Alameda Beach

Bay Farm Island

Pinole

Fremont

Hayward

Oakland

Benicia

Berkeley

Richmond

Martinez

Palo Alto

Sausalito

San Rafael

Redwood City

San Francisco

San Francisco Bay Subtidal Habitats

Major Eelgrass Beds

0 5

Miles

Eelgrass (Zostera marina)
﻿120 • San Francisco Bay Subtidal Habitat Goals Report

Seagrass beds generally are subject to several key limiting factors. First, the 

beds can be established only where the substrate is suitable, meaning a bottom 

composed of sand to mud, where current speeds and wave energy are not 

excessive, and where light penetration is sufficient (i.e., the water is not too 

deep or too turbid). The more turbid the water, the shallower the maximum 

depth at which seagrass beds can grow. The supply of seeds or seed-bearing, 

flowering shoots is important in establishing and maintaining beds (Duarte 

1991, Zimmerman et al. 1995). Seeds are denser than water and therefore 

transport of seeds across areas of deep water is limited (Orth et al. 1994). 

However, shoots break off and raft over considerable distances before rooting 

or dropping seeds (Harwell and Orth 2002). Once established, seagrass beds 

alter the substrate and reinforce their hold on the bottom by extending a network of rhizomes horizontally under the sediment, and produce new shoots 

vegetatively or by dropping seeds. The tendency of eelgrass to stabilize sediment, grow through shoots, and alter hydrodynamics provides for positive 

feedback, allowing an established bed to persist.

Figure 8-3: Conceptual diagram for eelgrass in San Francisco Bay.This diagram displays

processes that occur in and on eelgrass beds,some of the ecosystem services these habitats

provide, and threats to eelgrass beds.

 

Hardened 

shorelines reflect

waves and increase 

their effects. 

Sea level rise will 

amplify this effect.

 

 Wind waves, 

boat wakes, and 

currents increase 

 turbidity. 

Increased wave 

action breaks up

beds.

 Eelgrass

 converts sunlight 

to plant biomass, 

providing habitat

and food for 

 bay fauna.

Turbidity limits the depth where eelgrass can 

grow. Other disturbances include boat

anchorages, docks (shading), and contaminants.

Dredging, ferry and ship 

wakes may increase turbidity.

Beds naturally slow currents 

and trap sediment.

Bat rays and other animals disturb the bottom, 

 increasing turbidity.

Spilled oil can foul 

shallow beds and cause 

long-term damage.
Chapter Eight: Submerged AquaticVegetation • 121

Eelgrass Beds in the San Francisco Estuary

Appendix 8-1 provides a thorough analysis of the current state of knowledge of 

eelgrass beds in the estuary, including potential for restoration. Eelgrass beds 

provide shelter and food to small fishes of a variety of species, such as pipefish, staghorn sculpin, and three-spined stickleback (Grant 2009 for Elkhorn 

Slough). These include species that occupy eelgrass beds for their full life cycle 

(for example pipefish) and those that use eelgrass beds only as nurseries. The 

importance of this nursery habitat to the life histories of fish in San Francisco 

Bay is unknown, although the limited extent of the eelgrass suggests that the 

more abundant species do not depend on eelgrass beds for any part of their 

life cycles. Also, the extent to which eelgrass supports species of concern (for 

example Pacific herring, salmon) is not well known. A substantial increase in 

extent of eelgrass might provide resources for a wide variety of species.

Eelgrass is used as a substrate for spawning by Pacific herring, which lay sticky 

eggs on the plant’s blades as well as on macroalgae and pier pilings and other 

hard surfaces. Earlier surveys revealed that most spawning in the Central 

and South Bays took place on human-built structures, including pier pilings 

(Watters et al. 2004). However, recent surveys indicate that about half takes 

place on eelgrass and half on artificial structures (Isaac, CDFG, 2010, pers. 

comm.). Only in the Northwest Central Bay (e.g., Richardson Bay, Keil Cove) 

was there substantial spawning on submerged vegetation, indicating that 

spawning on eelgrass may be limited by the small current extent of beds in the 

spawning area. Since the creosote in pier pilings may inhibit development of 

herring embryos (Vines et al. 2000), the importance of eelgrass and possibly 

EELGRASS BED

Destruction Establishment

Invertebrates

Sediment 

Type

Waves

Dredging

Sea Level 

Rise

Attribute of physical structure

Threat to habitat

Other inuence on habitat 

Function or species 

inuenced by the habitat

Human-induced threat

Inuence generally causing 

increase in target

Inuence generally causing a 

negative effect upon target

Factor causing either increase 

or decrease in target 

3541 g. 8-4 submerged aqu

Available 

Habitat

Depth Range

Docks, Boating,

Shipping

Food for 

Fish Spawning Shelter for 

Fish

Food for 

Ducks, Geese

Sediment 

Trapping

Turbidity

Detrital 

Output

Figure 8-4: Influences on eelgrass beds and functions and services provided by eelgrass beds.

The elements in this diagram are site-specific, and all do not apply at all sites. See also Fig. 3 in

Thom et al. (2005).
﻿122 • San Francisco Bay Subtidal Habitat Goals Report

other SAV as subsequent recruitment to the herring population may be greater 

than indicated by the spawning surveys.

The significance of eelgrass beds as a food resource in the San Francisco 

Estuary is unknown. Primary productivity of Pacific Northwest eelgrass beds 

is on the order of 200-500 grams carbon per square meter per year (Phillips 

1984), which is higher than phytoplankton productivity in the San Francisco 

Estuary, which is around 100 grams carbon per square meter per year (Cole 

and Cloern 1984). Productivity of eelgrass in the San Francisco Estuary is 

currently being estimated (K. Boyer, SFSU, 2009, pers. comm.). However, the 

limited extent of eelgrass beds means that this extra productivity on an areal 

basis amounts to very little bay-wide. For example, if the productivity of eelgrass beds is four times that of phytoplankton, at the current areal coverage this 

amounts to only around 4% of phytoplankton productivity, well below the resolution of any method to measure it. Therefore, the only measurable impact of 

this productivity is likely to occur within and near the beds themselves, where 

the combination of complex physical habitat and high productivity should 

lead to high secondary productivity. This could change, were eelgrass beds to 

occupy a much larger fraction of their potential range.

Local food production may be important to ducks and geese that feed directly 

on eelgrass. In particular, brant geese feed almost exclusively on eelgrass in 

Humboldt Bay (Moore and Black 2006) and Morro Bay (Anonymous 2003). 

Although not common in San Francisco Bay, brant are seen mainly in eelgrass 

beds (J. Takekawa, USGS, 2009, pers. comm.). It has been reported that historically, brant congregated in large numbers in San Francisco and San Pablo Bays, 

but that the population decreased in San Francisco presumably because resources 

became limited (Grinnell and Miller 1944). Canada geese also feed on eelgrass 

and their grazing may have an impact on shoot survival and life history patterns 

(Appendix 8-1). Other birds that feed in eelgrass beds may depend on the eelgrass or on organisms within the beds (Baldwin and Lovvorn 1994).

The invertebrate fauna of eelgrass may be important resources to consumer 

organisms, including birds and both resident and transient fish. Amphipods 

Brant feeds on eelgrass at

Drake’s Estero.
Chapter Eight: Submerged AquaticVegetation • 123

were the most abundant invertebrates on eelgrass at several sites in San 

Francisco Bay in 2007 (Carr 2008, Carr et al. in press). Experiments in tanks 

showed a substantial effect of grazing by fish on amphipods, and substantial 

consumption of both epiphytes and eelgrass blades by amphipods when fish 

were excluded (Carr 2008). Thus, predation on invertebrates may be an important factor regulating the growth of eelgrass plants and the development of 

beds. The importance of this consumption to fish is unknown.

When eelgrass reproduces through seeds, generally in summer-fall, dispersal 

of seeds is facilitated by the movement of flowering shoots, which can float for 

up to two weeks and drop seeds for up to three weeks (Harwell and Orth 2002). 

The time scales for dispersal of eelgrass are shorter than estimates of water residence time in the estuary, which are up to 60 days for the northern estuary in 

summer and much longer for the South Bay (Walters et al. 1985). This implies 

that a large proportion of the seed-bearing shoots would be retained within 

the estuary. However, these shoots are highly subject to wind and wind-driven 

surface currents, which in late spring to fall implies movement generally from 

west to east.

Although eelgrass can establish in a range of sediment sizes where turbidity is 

low, once established, eelgrass beds trap mostly fine sediment and thereby further reduce turbidity. The importance of the sediment-trapping function of eelgrass in the San Francisco Estuary is unknown and likely to be localized given 

current levels of eelgrass coverage. As with productivity, this could change 

with a greater extent of eelgrass beds, and if the beds were more contiguous. 

Sediment trapping may be an important function of eelgrass beds that are 

planted as a part of living shorelines (see Chapter 10). Temperature and salinity 

can limit eelgrass distribution and growth. In other regions, high water temperatures can contribute to eelgrass mortality (Moore and Jarvis 2008), and wasting disease has been related to high temperature (Orth et al. 2006). Tidal currents and wind waves in many parts of San Francisco Bay are probably strong 

enough to prevent excessive warming; however, high temperatures have been 

measured on single dates in limited surveys within eelgrass beds to date (S. 

Kiriakopolos, unpublished data; Appendix 8-1). Salinity is a limiting factor for 

eelgrass beds, resulting in their absence farther up the estuary than Carquinez 

A moon jelly in an eelgrass bed.
﻿124 • San Francisco Bay Subtidal Habitat Goals Report

Strait. However, individual plants are tolerant of low salinity (Phillips 1984), 

and extended periods of low salinity (as in spring 2006) do not appear to have 

had a negative influence on extant beds. 

Eelgrass beds in the San Francisco Estuary are strongly limited in maximum 

depth by the high turbidity of the water. In contrast to many locations where 

eelgrass occurs, this turbidity is due not to phytoplankton but to inorganic 

mineral particles (Cloern 1987). Therefore competition for light between phytoplankton and eelgrass, a result of eutrophication in many estuaries, 

is not an issue in the San Francisco Estuary. Rather, growth of both phytoplankton and eelgrass are controlled by turbidity that depends on sediment 

supply from the rivers, wind waves, and circulation patterns. This may also 

limit overgrowth by macroalgae, which can otherwise occur in high-nutrient 

waters (Huntington and Boyer 2008), but has been seen only occasionally within eelgrass beds in San Francisco Bay (see Appendix 8-1, G. Santos, 

unpublished data.).

Threats to Seagrasses

Seagrasses in general are subject to many threats over short and long time 

scales (Figures 8-3 and 8-4), most due to human activities (Phillips 1984, Orth 

et al. 2006), and globally are in a state of decline (Waycott et al. 2009). The 

principal threat worldwide is probably eutrophication leading to excessive 

algal biomass and light limitation of seagrass growth (Orth et al. 2006). High 

temperatures associated with global climate change may increase incidence of 

wasting disease (Orth et al. 2006). Activities associated with shipping and boating can disrupt seagrass beds directly through destruction of plants by boat 

propellers, anchors and anchor chains, dredging, and construction of facilities 

(for example, docks, harbors, breakwaters, ports). Indirect effects arise through 

increased suspended sediments due to dredging and boat wakes, or shading 

from overwater structures such as docks. Hardening of the shoreline can reflect 

waves, increasing wave action and limiting or destroying beds.

Changing bathymetry or sediment composition and increasing water depth due 

to sea level rise, especially near hardened shorelines, can impede establishment 

of seagrass beds, cause restoration projects to fail, or damage or destroy existing beds. Development on adjacent shores can increase runoff of fresh water or 

contaminants or increase turbidity, all with negative impacts on seagrass beds. 

Invasive eelgrass (Zostera japonica) has caused habitat alterations in estuaries of 

the Pacific Northwest (Larned 2003) and is present in Humboldt Bay.

Most of these threats apply to eelgrass in the San Francisco Estuary but are 

focused in localized areas. For example, impacts from dredging seem to have 

a limited spatial and temporal extent (Schoellhamer 2002). Damage from boat 

anchors, shoreline development, and ship wakes is also likely to be localized 

(Figures 8-3 and 8-5). Oil spills can inundate and smother eelgrass beds, particularly those in the intertidal or shallow subtidal zones.
Chapter Eight: Submerged AquaticVegetation • 125

Figure 8-5: Locations of Submerged AquaticVegetation Stressors in San Francisco Bay.
﻿126 • San Francisco Bay Subtidal Habitat Goals Report

Rising sea level will affect eelgrass beds in several ways. Where the beds are 

located on a bottom that slopes gradually to the surface (Figure 8-6), rising sea 

level may enhance growth at the shallow end of the bed and reduce it at the 

deep end, resulting in an upward migration of the bed. However, much of the 

bay is bordered by seawalls or rock revetments, which would limit the landward extent of the beds. In these areas, rising sea level would cause a loss of 

eelgrass beds in the deeper sections without a concomitant gain in the shallows, possibly exacerbated by increased wave action due to reflection of waves 

off the seawalls.

Water clarity may be increasing as a result of the long-term decrease in suspended sediment concentration in the estuary (Schoellhamer 2009). This 

decrease is due mainly to the winnowing out of sediments deposited during 

hydraulic mining in the late 19th century (Jaffe et al. 2007, Schoellhamer 2009). 

The likely effects of a continuing increase in water clarity include an increase in 

phytoplankton productivity and a greater depth range over which eelgrass can 

survive, although quantitative projections of future outcomes for eelgrass are 

not yet possible. 

Rationale for Establishing Goals for SAV

Applying the approach outlined in Chapter 2, it is clear that the restricted 

extent of eelgrass beds may be limiting their support of valued ecosystem services. Furthermore, restoration has been demonstrated and is therefore feasible 

(Appendix 8-1), although questions remain about the anticipated trajectory 

of restoration and associated response of ecosystem functions and services. 

3541 fig. 8-6 hypsographic curve Depth (Meters Below Mean Higher High Water)

0

Percentage of Area Shallower 

Than Water Depth

20 40 60 80 100

120

80

30

40

50

20

0

10

Suisin Bay

Carquinez Strait

San Pablo Bay

Central Bay

South Bay

Figure 8-6: Hypsographic curve for the major basins of the San Francisco Estuary (Kimmerer

2010). Each line gives the percent of the geographic area of the basin (x axis) that is shallower than

the depth (y axis) below Mean Higher HighWater. Symbols indicate deepest depths in each basin.

All basins have extensive regions of shallow water (e.g., 79% of the area of San Pablo Bay is 5m or

less).The boundary between Central and South San Francisco Bay was set at the Bay Bridge. Data

from USGS bathymetricWeb site: http://sfbay.wr.usgs.gov/sediment/sfbay/downloads.html.
Chapter Eight: Submerged AquaticVegetation • 127

Therefore, restoration is warranted for eelgrass beds, 

but should be done within an experimental framework (see Adaptive, Phased Approach below, and discussion of adaptive management in Chapter 2).

Goals for eelgrass beds focus on protecting and 

enhancing existing eelgrass beds, creating additional 

eelgrass beds, and improving our understanding of 

ecosystem services, factors influencing the beds, and 

methods for restoration. Protection goals for eelgrass 

include protective buffers around eelgrass beds and 

proposed eelgrass reserves. The recommended protective buffer around eelgrass beds has been determined 

provisionally based on expert opinion (K. Boyer, 

SFSU, 2009, pers. comm. and K. Merkel, Merkel and 

Associates, 2009, pers. comm.), although some habitat 

function and ecosystem services provided by eelgrass 

beds can extend beyond this protective buffer. For 

example, waterfowl congregate within several hundred 

meters of eelgrass. The Subtidal Goals Project recommends protecting existing, established eelgrass beds 

by establishing eelgrass reserves. While establishment 

of eelgrass reserves at selected locations is included 

as a goal, specific details about how such reserves are 

established and ultimately function are purposefully 

not included here and should be developed as part 

of the process that implements the reserves. Eelgrass 

is the only habitat type the Subtidal Goals Project recommends protecting 

through habitat reserves.

The principal restoration goal, pending a satisfactory determination of its benefit, is to restore large areas of eelgrass based on habitat suitability determined 

by modeling studies (Merkel and Associates 2005). The 50-year maximum 

restoration targets below are based on the acreage of nearshore areas with 

moderate to high suitability according to indices of the model. Native eelgrass 

would be restored not throughout these target areas, but at a subset of locations 

within these larger areas. The target acreage would increase eelgrass distribution within 50% of identified potential habitat. The long-term acreage targets 

were developed with the assumption that without restoration efforts eelgrass 

acreage will remain relatively stable. Should eelgrass acreage increase considerably independent of restoration efforts, such increase should count towards the 

overall acreage target. 

In keeping with the Subtidal Goals Project’s precautionary approach, protection 

goals for other species of SAV, including widgeon grass and sago pondweed, are 

included while research is conducted to better inform our need for restoration 

or protection of these non-eelgrass SAV habitats. 

Eelgrass beds can be found at Keller

Beach in Miller Knox Regional

Shoreline in Point Richmond.
﻿128 • San Francisco Bay Subtidal Habitat Goals Report

Adaptive, Phased Approach to Eelgrass Restoration

An adaptive approach to restoration, conducted in phases from small scale 

to large (Appendix 8-1), would have two key advantages. First, the effort can 

begin at small enough scales to be experimentally and logistically tractable and 

to allow for the learning necessary to expand the scale of restoration projects in 

subsequent phases. Second, within a program of adaptive management, pursuing restoration in phases can ensure that information is gathered to answer the 

fundamental questions about the roles of eelgrass (i.e., questions under Science 

Goal 1, below) and the responses of eelgrass beds to environment (Science 

Goal 2), as well as questions related to restoration itself (Science Goal 3). That 

is, at each phase, investigations into the roles and responses of eelgrass beds 

and the relationship of these to the scale of the restoration will be embedded in 

any significant restoration project.

The phased approach begins by selecting sites for experimental restoration 

projects, to refine site selection and restoration methods. Results from this 

phase will be used to design the pilot phase, which will scale methods to larger 

areas and also begin to gather evidence about the likely outcomes of restoration. Depending on results from the pilot phase, restoration could be attempted 

at larger sites, with each step being contingent on the development of evidence 

in previous phases indicating a high value for restored eelgrass beds (for example a high level of use by herring or other fishes of concern).

The knowledge developed during each phase will be critical for answering the 

key research questions enumerated below. These include determining the effectiveness of eelgrass restoration in providing valued ecosystem services, the environmental controls on eelgrass beds, and the methods that will maximize the 

success of the restoration. Of these questions, the most critical is the provision 

of ecosystem services, since this is the justification for attempting restoration 

beyond the experimental scale. Thus, our understanding of the extent of ecosystem services provided by restored eelgrass beds must be improved substantially 

at each phase beyond the experimental phase, before the process moves into the 

next phase. To continue restoration without this knowledge would risk not only 

wasting public money if the restoration proves ineffective, but could also jeopardize support for these and other restoration activities.

Criteria for site selection include local conditions (for example depth profile, 

sediment type, waves and currents, salinity patterns, turbidity) and the environmental context (for example proximity to hardened shorelines, ports or 

piers, proximity to source beds for seeds, convenience for planting and monitoring), taking into account likely changes in these attributes with long-term 

trends such as sea level rise and increasing water clarity. Initial work on this 

has been completed (Appendix 8-1). The phases listed here are based on those 

enumerated in Appendix 8-1, with the added consideration of bay-wide science 

goals (see below) and the need to address fundamental questions about the 

value of restored eelgrass beds as restoration progresses. Thus, the phases have 

Native Eelgrass

Monitoring and

Restoration Pilot

Projects to Date

• UC Berkeley,William Setchell

surveys: 1923–1929

• University ofWA, Sandy

Wyllie-Echeverria surveys,

common garden: 1986, 1987

• Wyllie-Echeverria and Rutten

1989

• Wyllie-Echeverria and Kitting

1990

• Fonseca et al. 1998

• Hanson 1998

• Merkel 2003, 2009

• Boyer et al. 2005–2010
Chapter Eight: Submerged AquaticVegetation • 129

Phases in an SAV RESTORATION EFFORT

Phase I. Experimental restoration

This phase will develop the experimental design for the

restoration to answer key questions about sites and methods

(science goals).The phases within this group should be

followed in sequence but can be accomplished for different

sites at different times.

Phase I-1: No prior knowledge of site

Conduct a basic site survey.

Phase I-2: Limited site knowledge

Condition: Mapping or surveys have been conducted.

• Assess suitability of the site for restoration.

Phase I-3: Experimental restoration

Condition: Phase 1-1 and 1-2 actions completed; area is unlikely

to recruit naturally and is suitable.

• Determine experimental design to fit the site.

• Establish replicated small-scale test plots at various

elevations, donors, and other treatments.

• Evaluate outcomes: plant persistence,spread, abiotic

conditions, use by other organisms.

• Include evaluation of restoration potential and lessons

learned in a report.

Following this phase an evaluation takes place in which

decisions are made about whether and to what extent

to proceed into pilot restoration.This decision should be

made largely on the basis of feasibility and conditions at

individual sites.

Phase II: Pilot restoration

This phase will expand on the previous experimental phase to

determine the suitability of alternative methods of restoration

at a larger scale than the experimental scale. It will also begin

to evaluate the larger implications of restoration for its value

in increasing the provision of ecosystem services (science

goals 1 and 2 below).

Condition: Phase I has been completed for candidate site, and

site remains suitable.

• Design small pilot restoration project (0.5 acre or less)

to test hypotheses developed or provisionally tested in

Phase I.

• Include explicit measures to determine quantitatively the

use of the restored site by organisms and other evidence

about the likely benefits of restoration in the design.

• Establish replicated moderate-scale test plots.

• In the second year of the program, begin to assess aspects

of ecosystem function (e.g.,spawning substrate and

nursery and foraging habitat).

• Evaluate outcomes including those in Phase I, and aspects

of ecosystem function.

• Include evaluation of restoration potential, value, and

lessons learned in a report.

Following this phase an evaluation takes place in which

decisions are made about whether and to what extent

to proceed into larger-scale restoration.The decision

about whether to expand the scale of restoration should

be based on an assessment that the restored eelgrass

beds likely provide ecosystem services commensurate

with the cost and effort involved in the restoration.This

decision could be made provisionally on the basis of a few

pilot projects, and re-evaluated as more pilot projects are

completed.The decisions about where and how to restore

should be based on lessons learned from individual sites

about feasibility and conditions.

Phase III. Larger-scale restoration project

This phase will expand on the pilot phase with the

principal purpose being to evaluate the larger implications

of restoration for its value in increasing the provision of

ecosystem services (Science Goals 1 and 2 below).This phase

will also determine how alternative methods of restoration

scale up beyond the pilot scale.

Condition: Phase II has been completed for candidate site, and

site remains suitable.

• Design intermediate-scale restoration project (~1 acre)

to answer questions under Science Goals 1 and 2, and to

further develop the art and science of eelgrass restoration.

• Include explicit measures to determine quantitatively the

use of the restored site by organisms and other evidence

about the likely benefits of restoration in the design.

• Establish replicable larger-scale test plots.

• In the second year of the program, begin to assess aspects

of ecosystem function (e.g.,spawning substrate and

nursery and foraging habitat).

• Evaluate the response of ecosystem functions and likely

ecosystem services.

• Include evaluation of restoration potential, value, and

lessons learned in a report.

If the value of the restoration as estimated in this phase

continues to suggest further expansion, this phase may

be repeated at different sites as pilot programs are

completed, and the acreage target expanded at each

site and the above process repeated.The decision about

whether to expand the scale of restoration should be

based on an assessment that the restored eelgrass beds

likely provide ecosystem services commensurate with the

cost and effort involved in the restoration.This decision

would remain provisional with additional information

coming in as pilot and then larger-scale projects are

completed.The decisions about where and how to restore

should be based on lessons learned from individual sites

about feasibility and conditions.

At this scale a critical issue is the long-term viability of the

restored eelgrass beds and their provision of ecosystem

services.
﻿130 • San Francisco Bay Subtidal Habitat Goals Report

been expanded to encompass steps in an adaptive management program. See 

Appendix 8-1 for methods that may be applied in each phase.

Science Goals for SAV

Most of the science questions for SAV parallel those for shellfish, so much 

of the information below is duplicated in both sections. Goal 1 also applies 

to other SAV beds not covered explicitly here, although these may be assigned a 

lower priority given the greater extent of, and research interest in, eelgrass beds.

Submerged Aquatic Vegetation Science Goal 1

Understand the ecosystem services the eelgrass beds support, 

and in what quantities, in their current state and after 

restoration.

Question A. What specific functions do eelgrass beds support?

This question could be addressed in part by an examination of extant beds 

in different parts of the bay, supplemented by lessons learned during early 

restoration.

Question B. How much is attributable to the structure vs. the plants? 

The basis for this question is discussed above. 

Question C. How do the functions of restored eelgrass beds scale with the total 

area restored?

If eelgrass beds are being restored to support ecosystem services, enough beds 

must be restored to provide a substantial increase in these services. These services may scale linearly with the increase in bed area, or some other way (see 

Figure 2-2 in Chapter 2). For example, there may be a threshold of bed area 

above which some part of the ecosystem shifts into a different, preferable state, 

in which case the cumulative restoration must exceed the threshold before this 

benefit is achieved.

These subtle interactions would be difficult to determine, particularly before 

restoration began. Assuming a linear response, though, it should be possible to 

calculate the extent or value of an ecosystem service of existing natural or previously restored eelgrass beds, perhaps in terms of food, structural habitat for 

fishes and birds of concern, and shoreline protection per unit area or shoreline 

distance. This information could be used to project the value of the restored 

habitat, and to update this projection with newly gathered data. This projection should be done assuming that the functions of eelgrass beds may vary 

geographically.

A corollary of this question is how does the degree of fragmentation of the 

habitat influence its function, i.e., does a series of fragments perform the same 

function as a contiguous habitat of the same area?

San Francisco State University

researchers get ready to monitor

eelgrass.
Chapter Eight: Submerged AquaticVegetation • 131

Submerged Aquatic Vegetation Science Goal 2

Understand the factors controlling the development and 

persistence of eelgrass beds.

Question A. How do individual beds respond to their local biotic and abiotic 

environment?

Salinity, temperature, wind and wave patterns, currents, sediment delivery, and 

consumption may all play a role in the growth or shrinkage of eelgrass beds. 

However, these influences are understood only at the most basic level.

Question B. What limits the establishment of new beds, either under natural conditions or as restoration projects?

Eelgrass can establish most readily in shallow water sediments. Sandy sediments are usually associated with strong currents or wind waves that winnow 

out the finer particles, whereas muddy sediments are associated with high 

turbidity. Therefore, eelgrass may establish only under rare conditions, such 

as a period of neap tide with light winds (necessary for the plants to stay put) 

following a spring tide with storms that sort the sediment. Once a bed is established, it traps sediments, and the grain size becomes progressively finer without impairing the bed. Therefore it may be possible to establish beds in areas of 

fine-grained sediments, provided the other limiting factors are minimized. 

The native sea slug Phyllaplysia sp. lives 

in eelgrass beds in San Francisco Bay.
﻿132 • San Francisco Bay Subtidal Habitat Goals Report

Question C. How do estuarine currents including wind-driven circulation influence the movement of seed-bearing shoots and subsequent recruitment?

Once beds have been established, the potential exists for them to send seeds to 

other areas of the estuary and to establish remote daughter beds. This potential 

depends on duration of the dispersive stage and the very specific details of circulation both at the scale of the beds themselves and at a broader scale.

At the scale of estuarine basins or even the whole estuary, regions of high 

abundance of mature eelgrass plants are likely seeding those of low abundance, 

and the supply of seeds at any one location may have little to do with the abundance of mature plants at that location. Large restoration sites may therefore 

contribute to settlement and even establishment of beds in remote locations 

provided the substrate is available and the local and regional currents are favorable. At the scale of individual beds, the rate of settlement is likely affected by 

local conditions. 

Question D. What is the degree of connectivity among beds?

The previous question can be turned around: how do population and genetic 

structure vary among beds, and what can that tell us about the connectivity 

among beds? This is a particularly important component for understanding the larger-scale issues raised under Goal 1, Question C. Note that genetic 

structure and ecologically relevant population structure are likely to be different and operate at different scales, and require different tools for investigation. 

Research to date indicates considerable genetic structure among eelgrass beds, 

implying low connectivity and possibly selection based on local conditions. 

This must be considered in collecting donor material for restoration.

Question E. How do size of and density in a bed, and fragmentation of beds, 

influence persistence and expansion?

Beds vary in space and time in their spatial extent, shoot density, and degree of 

fragmentation. The factors that produce these changes and the effect of these 

changes on persistence of beds are unknown. For example, is a decrease in 

shoot density a harbinger of bed collapse and under what conditions? 

Question F. What is the extent of mortality in eelgrass beds due to exogenous factors and what controls die-back and recovery?

Eelgrass beds do not seem very susceptible to low salinity, but the size and 

extent of beds can vary substantially from year to year, through some combination of die-back, seeding, and vegetative growth. 

Canvasbacks congregate in

large numbers in eelgrass beds

in the bay.
Chapter Eight: Submerged AquaticVegetation • 133

Submerged Aquatic Vegetation Science Goal 3

Develop the most effective ways of restoring and protecting 

eelgrass beds.

Question A. How do physical structures, spacing, and orientation of restored beds 

interact with the local environment to influence the rate of seed and vegetative 

shoot settlement and survival?

Local conditions including salinity, currents, and the supply rate of sediment 

and seeds are likely to influence settlement and survival. Design of eelgrass 

beds may influence settlement and survival differently depending on these 

local conditions. Therefore lessons from one site may not be entirely transferable to another. 

Question B. What is the influence of grazing disease, and algal overgrowth on the 

success of restoration?

Disease has not yet been identified as a significant factor in the dynamics of 

eelgrass populations in the estuary. This could change with increasing population density, and effects are likely to be sporadic and therefore difficult to detect 

and assess. Consumption by grazers is both a source of mortality and a means 

by which the beds support ecosystem processes, so some amount of consumption is consistent with “success.”

Question C. How can beds be designed and built so as to minimize the need for 

ongoing intervention?

Minimizing human intervention would reduce the cost of restoration and 

increase the likelihood of long-term persistence of the beds. This does not 

eliminate the need for periodic monitoring.

Question D. How do oyster beds and eelgrass beds interact, and how do they 

interact with other habitats?

Since some of the functions of eelgrass and oyster beds are similar, there may 

be advantages to establishing them in close proximity. Also, restoration should 

take into account potential negative effects on other habitats or values, or on 

eelgrass beds because of other habitats.

Kayaks are an efficient,shallow draft

boat used to access shallow subtidal

areas in the bay. Richardson Bay

Audubon conducted GPS surveys of

eelgrass beds in Richardson Bay in

2006; this model could be expanded

to include volunteers who want to

monitor additional eelgrass beds in

the bay.
﻿134 • San Francisco Bay Subtidal Habitat Goals Report

Question E. How do wind waves, wakes, and turbidity affect eelgrass beds?

Wave action can affect beds directly or through increases in turbidity. Better 

information on the extent to which vessel wakes and turbidity disrupt eelgrass 

beds can inform the potential use and size of buffer zones to limit this damage.

Question F. Where and when do introduced species or macroalgal blooms damage 

or degrade eelgrass beds?

Disruption by potential introduced species such as the eelgrass Z. japonica

could be considerable, and early detection is necessary to allow eradication to 

be attempted. Macroalgal blooms also have the potential to damage eelgrass. In 

other locations where algal blooms threaten seagrasses, the principal cause of 

the blooms is excessive nutrient loading. That is not the case in San Francisco 

Bay, where turbidity severely limits plant growth and nutrient concentrations 

are usually high. However, algal blooms might be stimulated by an increase 

in water clarity either due to the action of the eelgrasses themselves, or to 

broader-scale changes in sediment loads or distribution.

Question G. What are the best methods and timing for eelgrass restoration that 

minimize settlement of invasive species?

Submerged Aquatic Vegetation Science Goal 4

Assess the status and distribution of other SAV.

Question A. What is the distribution and abundance of each of the native SAV 

species other than eelgrass?

Protection Goals for SAV

Submerged Aquatic Vegetation Protection Goal 1

Protect existing eelgrass habitat in San Francisco Bay through 

no net loss to existing beds. (Baseline is considered to be 3,700 

acres in October 2009.) 

•	 Eelgrass Beds Protection Objective 1-1: Promote protection of eelgrass 

beds through collaboration with the boating community. 

Submerged Aquatic Vegetation Protection Action 1-1-1: Develop and use best 

boating practices to reduce impacts from propellers, anchors, and anchor 

chains.

Promote stewardship of eelgrass by placing educational materials and signs 

at marinas. Collaborate with the boating community to develop no-wake 

zones and avoidance areas to preserve eelgrass habitats. Place markers or 

buoys around eelgrass beds to demarcate the slower speed zone and the 

presence of eelgrass.
Chapter Eight: Submerged AquaticVegetation • 135

Submerged Aquatic Vegetation Protection Action 1-1-2: When developing new 

ferry routes and terminals locate them away from existing eelgrass beds.

Submerged Aquatic Vegetation Protection Action 1-1-3: Replace existing 

permitted moorings within or adjacent to (150 feet) existing eelgrass beds 

with non-dragging mooring chains. Remove unpermitted moorings within 

and adjacent to (150 feet) of eelgrass beds. 

Submerged Aquatic Vegetation Protection Action 1-1-4: Locate new mooring 

areas at least 150 feet away from existing eelgrass beds. 

Submerged Aquatic Vegetation Protection Action 1-1-5: Anchor barges or vessels 

outside of existing eelgrass habitat. 

•	 Submerged Aquatic Vegetation Protection Objective 1-2: Support 

preservation of existing eelgrass beds by locating new or reconstructed 

structures (for example docks, piers) or new dredging projects away from 

eelgrass beds.

Submerged Aquatic Vegetation Protection Action 1-2-1: For new or expanded 

docks or structures, encourage placement at a minimum of 150 feet from 

existing eelgrass beds. 

Submerged Aquatic Vegetation Protection Action 1-2-2: Promote use of light 

transmitting materials and techniques (for example grating, spacing between 

deck boards) in dock and pier reconstruction projects. 

Submerged Aquatic Vegetation Protection Action 1-2-3: For new dredging 

projects, encourage placement outside existing eelgrass beds and not closer 

than 150 feet.

Recreational boaters can protect

eelgrass beds by not anchoring

directly in the beds, and taking care

to prevent accidental groundings.
﻿136 • San Francisco Bay Subtidal Habitat Goals Report

Submerged Aquatic Vegetation Protection Goal 2

Establish eelgrass reserves.

•	 Submerged Aquatic Vegetation Protection Objective 2-1: Establish 

eelgrass reserves for existing eelgrass beds with unique qualities (for 

example oldest beds, extensive history of research, donor populations, 

value to fisheries). Potential reserve sites include the following eelgrass beds:

· Keil Cove

· Point San Pablo

· Point Molate

· Richardson Bay

· Crown Beach 

· Bay Farm Island

· Eden Landing Ecological Reserve

· Coyote Point

Submerged Aquatic Vegetation Protection Action 2-1-1: Develop a committee 

to identify, implement, and evaluate a mechanism for establishing and 

managing the eelgrass reserves, and any potential areas for future eelgrass 

reserve designation.

Submerged Aquatic Vegetation Protection Goal 3

Identify and protect areas in San Francisco Bay for future 

eelgrass expansion, restoration, or creation. 

•	 Submerged Aquatic Vegetation Protection Objective 3-1: Maintain and 

improve physical conditions (for example to bathymetry, light availability, 

currents) needed to support eelgrass survival and growth in areas identified 

in this report for future eelgrass restoration.

•	 Submerged Aquatic Vegetation Protection Objective 3-2: Purchase 

subtidal property from willing sellers or create conservation easements 

for eelgrass beds that are privately owned. (Potential sources of funding 

may include but are not limited to The Nature Conservancy, State Coastal 

Conservancy, Audubon, Coastal Estuarine Land Conservation Program, 

land trusts, etc.). 

Submerged Aquatic Vegetation Protection Goal 4

Protect existing widgeon grass habitat in San Francisco Bay.

Widgeon grass bud/emerging flower.

Fruiting sago pondweed.
Chapter Eight: Submerged AquaticVegetation • 137

Submerged Aquatic Vegetation Protection Goal 5

Protect existing sago pondweed habitat in San Francisco Bay. 

Restoration Goals for SAV

Submerged Aquatic Vegetation Restoration Goal 1

Increase native eelgrass populations in San Francisco Bay 

within 8,000 acres of suitable subtidal/intertidal area over a 50-

year time frame using a phased approach under a program of 

adaptive management.

•	 Submerged Aquatic Vegetation Restoration Objective 1-1: Implement 

a program of adaptive management with phased restoration. Periodic 

reviews will determine whether the knowledge is adequate to support 

proceeding to the next phase. Provisionally the targets would be to increase 

native eelgrass habitat by 25 acres within 5 years, 100 acres within 10 years, 

and up to 8,000 acres within 50 years, at 35 locations. (See site list below, and 

more detail in Native Eelgrass Restoration Table in Appendix 8-1 for sitespecific phased actions.)

Submerged Aquatic Vegetation Restoration Action 1-1-1: Establish an objective 

review panel to evaluate evidence and make recommendations on stepping 

through phases of restoration.

Submerged Aquatic Vegetation Restoration Action 1-1-2: Develop a 

programmatic environmental review and permitting process to facilitate 

subtidal restoration projects, including native eelgrass restoration projects, 

to achieve multiple habitat and shoreline protection objectives. 

The following site recommendations are based largely on the recommendations 

from previous monitoring and restoration projects, one San Francisco Bay 

native eelgrass workshop in 2006, and from participants in an eelgrass restoration workshop held in Tiburon, California in December 2008.

Left:“Seed bags”—mesh bags with

eelgrass seeds from donor beds—are

used to create new eelgrass beds.

Right: Seed bags are hung from buoys

at restoration sites, where the seeds

drop and propagate eelgrass.
﻿138 • San Francisco Bay Subtidal Habitat Goals Report

Priority native eelgrass survey and restoration sites:

•	 Corte Madera Bay near the Corte Madera and Muzzi Marshes

•	 San Rafael shoreline to quarry near Point San Pedro

•	 Horseshoe Cove, Sausalito

•	 Richardson Bay

•	 West of Point San Pedro along the shoreline of China Camp State Park

•	 North Richmond Bed from Richmond Bridge to Carquinez Bridge

•	 Albany and Berkeley shorelines

•	 Emeryville Crescent

•	 Middle Harbor, Oakland

•	 Alameda Naval Air Station

•	 Hayward Shoreline

•	 Eden Landing Ecological Reserve

•	 Coyote Point area, San Mateo

•	 Near Piers 94 and 98, San Francisco

See Figure 8-7 for a map of existing and proposed sites for eelgrass restoration. 

•	 Submerged Aquatic Vegetation Restoration Objective 1-2: Incorporate 

native eelgrass restoration into other regional restoration and shoreline 

protection projects and initiatives.

Submerged Aquatic Vegetation Restoration Action 1-2-1: Initiate pilot subtidal 

integration projects that incorporate native eelgrass. 

Algae grows on eelgrass blades.
Chapter Eight: Submerged AquaticVegetation • 139

Figure 8-7: Recommended sites for phased native eelgrass restoration in San Francisco Bay.
﻿140 • San Francisco Bay Subtidal Habitat Goals Report

Submerged Aquatic Vegetation Restoration Action 1-2-3: Support public–private 

partnerships to restore native SAV. Work with regional organizations 

and agencies to identify partners who could incorporate native eelgrass 

restoration and monitoring into existing or planned projects. Possible 

partners include the San Francisco Bay Joint Venture, California 

Department of Fish and Game, the Wildlife Conservation Board, industry, 

and others.

Submerged Aquatic Vegetation Restoration Action 1-2-4: Incorporate San 

Francisco Bay eelgrass restoration goals into national restoration strategies, 

such as SeaGrass.net monitoring and NOAA Restoration Center programs.

Submerged Aquatic Vegetation Restoration Action 1-2-5: Incorporate existing 

eelgrass beds into fish tracking studies conducted through the Long Term 

Management Strategy Science Work Group.

Eelgrass in Richardson Bay.
 141

CHAPTER NINE

Macroalgal Beds

Beds of macroalgae constitute the third biogenic habitat 

along with submerged aquatic vegetation and shellfish beds in San 

Francisco Bay and are by far the smallest in total extent. Four species 

of macroalgae were listed by NOAA (Schaeffer et al. 2007) as sufficiently 

abundant to form beds: Ulva spp., Gracilaria pacifica, Fucus gardneri, and the 

introduced Sargassum muticum. The extent and characteristics of algal beds in 

San Francisco Estuary are poorly known. Together, Silva (1979) and Josselyn 

and West (1985) reported 162 species of macroalgae in San Francisco Bay of 

which 33 were estuarine and the remainder characteristic of the California 

coast. Five species have been reported as introduced in the bay. No quantitative 

analysis of the extent of subtidal beds has been conducted, although a subtidal 

Laminaria (kelp) bed has been identified off Raccoon Strait. Efforts have been 

made to eradicate the North Atlantic brown alga Ascophyllum nodosum from 

the bay (Miller et al. 2004). A seasonal survey of macroalgal abundance and 

species composition within eelgrass beds is underway (see Appendix 8-1).

Brown “feather boa” kelp, Egregia 

menziesii, occurs in the more marine 

regions of the Central Bay.
﻿142 • San Francisco Bay Subtidal Habitat Goals Project

Like eelgrass beds, macroalgal beds provide both physical habitat and food for 

numerous organisms (Figures 9-1, 9-2). Also like eelgrass beds, subtidal macroalgal beds can alter flow fields, providing small organisms with shelter from 

currents and predators, and can trap sediments, alter sediment chemistry, and 

provide a substrate for spawning. The red algae, Gracilaria/Gracilariopsis spp., 

are important substrate for herring roe in the bay (Ryan Watanabe, CDFG, 

pers. comm.). Intertidal macroalgae can retain water, providing a refuge for 

intertidal organisms like juvenile Dungeness crabs during low tides. 

Although algal beds constitute biogenic habitats, it is not clear whether they are 

always a desirable habitat. Beds of some macroalgae, including Ulva spp. and 

Gracilaria pacifica, can form nuisance blooms in response to high nutrient concentrations, and may overgrow eelgrass and interfere with their photosynthesis. 

However, to date there is little evidence of the formation of nuisance blooms in 

the bay, although Nichols (1979) did report decaying mats of algae in the South 

Bay in the summer of 1975. 

Spilled oil can foul 

shallow beds and cause 

long-term damage.

If water becomes clearer, 

algae can bloom with high

nutrients and outcompete

eelgrass for light. 

Herring spawn in 

Gracilaria beds.

Shorebirds forage in intertidal areas for food and 

harvest algae for nests.

Amphipods, sh, and mollusks

nd food and shelter in beds.

Ulva grows in protected, 

clear water with little 

motion and high nutrients. 

Laminaria is found in deeper water, 

attached to rock outcrops.

Impact from human 

trampling and collecting.

 

 Wind waves, 

boat wakes, and 

currents increase 

 turbidity. 

Shading from structures limits light

for algae growth.

PA

C I F I C

OC EAN

Figure 9-1: Conceptual diagram for algal beds in the San Francisco Estuary. This diagram displays

processes that occur in and on algal beds,some of the ecosystem services these habitats

provide, and threats to algal beds.
Chapter Nine: Macroalgal Beds • 143

Conceptual Model for Macroalgal Beds

In contrast to eelgrass, many macroalgae provide a suitable food source to a 

variety of grazers, predominantly macroinvertebrates. At least one amphipod 

species, Amphithoe valida, readily consumes Gracilaria sp. (K. Boyer, SFSU, 

2009 and 2010, pers. comm.). Gulls and cormorants will pick macroalgae 

from the intertidal beach wrack to line their nests. The wrack produced by 

macroalgae is an important food source for invertebrates living interstitially 

on beaches, mudflats, and marshes. These invertebrates in turn provide a food 

source for shorebirds and many other species along the shore. In contrast to 

tropical regions where many herbivorous fish species feed on macroalgae, a 

relatively small number of fish species in temperate regions use macroalgae 

as a substantial part of the diet. The topsmelt, Atherinops affinis, common in 

San Francisco Bay, can feed on macroalgae (Logothetis et al. 2001). There is no 

published information on the importance of algal beds in support of populations of consumer organisms in the bay. 

Estuarine species of macroalgae differ greatly in morphology, biochemistry, 

and habitat requirements. Some species of macroalgae are abundant in rocky 

high-energy sites with strong currents and breaking waves. Others are more 

abundant in protected waters, where they can form beds on soft substrate (Josselyn and West 1985). Some macroalgae can have very high nutrient uptake 

rates that do not saturate (Kamer et al. 2004) and can therefore take advantage 

of the usually high nutrient concentrations in San Francisco Bay (Cloern 1999, 

but see Dugdale et al. 2007). The high turbidity of the bay may inhibit algal 

bloom formation as it does for phytoplankton and eelgrass, except in intertidal 

areas. In addition, low-salinity pulses likely reduce the viability of algal beds 

within the estuary, particularly outside of the Central Bay, but stress on macroalgae from high and low temperatures is unlikely except in sunny intertidal 

ALGAL BED

Available 

Habitat

Sediment

Type

Attribute of physical structure

Threat to habitat

Other influences on habitat

Function or species 

influenced by the habitat

Human-induced threat

Influence generally causing 

increase in target

Influence generally causing a 

negative effect upon target

Factor causing either increase 

or decrease in target 

3541 fig. 9-2 algal bed

Turbidity

Macroinvertebrates

Fishing

Access Fish

Waves Shipping,

Dredging

Salinity

Temperature Nutrients

Figure 9-2: Influences on macroalgal beds and functions and services provided by algal beds.The

elements in this diagram are site- and species-specific, and all do not apply at all sites.

Many common seaweeds can be

found in San Francisco Bay, including

sea lettuce (Ulva spp.),rockweed

(Fucus gardneri), and Turkish towel

(Gigartina papillata).
﻿144 • San Francisco Bay Subtidal Habitat Goals Project

locations. The distributions and local abundances of macroalgae likely vary as 

these influences vary.

The greatest concern over algal beds seems to be their propensity to respond 

to eutrophication by overgrowth and expansion, i.e., forming nuisance blooms 

(Valiela et al. 1997). Large blooms of macroalgae have a negative impact on 

eelgrass in Tomales Bay (Huntington and Boyer 2008). However, surveys of 

macroalgae on eelgrass beds in San Francisco Bay revealed only occasional 

instances where the macroalgae were likely to impede growth of the eelgrass 

(see Appendix 8-1). There have been few reports of nuisance blooms in the bay. 

This could change if turbidity of the water decreases further (Schoellhamer 

2009). In addition to eutrophication, intertidal algal beds are vulnerable to 

other human disturbances such as trampling and recreational harvesting, as 

well as oil spills and the use of dispersants during cleanup (Foster et al. 1998).

Rationale for Establishing Goals for Macroalgal Beds

Applying the decision tree in Chapter 2 (Figure 2-1) to macroalgae, it is not 

clear that additional macroalgal beds would be beneficial, nor is it clear that 

macroalgal beds are in short supply. It is difficult to distinguish algal beds that 

support ecosystem services from those that interfere with these services. Since 

we do not know enough to make a definitive statement, the decision tree leads 

us to the need for more research as the most suitable outcome. Applying the 

precautionary approach adopted for this project, existing beds should be protected while research to improve our knowledge is conducted.

Goals for macroalgal bed habitat focus on conducting research, protecting 

existing non-nuisance beds, enhancing the beds by removing invasive species and debris, and improving our understanding of ecosystem services, bed 

dynamics, and nuisance versus non-nuisance beds.

Feather boa kelp on the shores of

Angel Island.
Chapter Nine: Macroalgal Beds • 145

Science Goals for Macroalgal Beds

Macroalgal Beds Science Goal 1

Understand the roles of macroalgal beds of different species 

in providing ecosystem services or interfering with services 

provided by other habitats.

Question A. What is the current extent of macroalgal beds by species?

A survey to determine the extent of the macroalgal beds is needed to allow for 

an understanding of their roles, species composition, including introductions 

of new species, impacts on the estuarine ecosystem, and vulnerabilities, for 

example, to oil spills. 

Question B. What ecosystem services do macroalgal beds support, and in what 

quantities?

If the extent of algal beds is very small, the magnitude of any services is also 

likely to be small. However, initial estimates of the area of beds (Question A) 

combined with rough estimates of the magnitude of functions, such as spawning habitat for herring, would provide a context for assessing the overall role of 

algal beds.

Question C. To what extent, and in what densities of which species, do algal beds 

or growths interfere with other habitats or form nuisance blooms?

Algae may overgrow eelgrass or oyster beds and potentially other habitats. This 

may result in reduced growth and possibly the survival of eelgrass and oysters.

Macroalgal Beds Science Goal 2

Understand changes in the extent or condition of macroalgae.

Question A. How do the beds change with changing conditions?

It would be useful to understand any trends toward a larger or smaller extent of 

algal beds, and particularly the reasons for these trends.

Sea lettuce on the subtidal shores of

East Marin Island.
﻿146 • San Francisco Bay Subtidal Habitat Goals Project

Protection Goals for Macroalgal Beds

Macroalgal Beds Protection Goal 1

Protect San Francisco Bay Fucus beds through no net loss to 

existing beds.

(See Rock Habitats Protection Objectives 1-1 and 1-2.)

Macroalgal Beds Protection Goal 2

Protect San Francisco Bay Gracilaria beds through no net loss 

to existing beds.

(See Rock Habitats Protection Objectives 1-1 and 1-2.)

Restoration Goals for Macroalgal Beds 

We do not have enough information about existing macroalgal bed distributions and threats to make specific restoration goals for this habitat type. (See 

experimental techniques described in Chapter 3: Cross-Habitat Invasive 

Species Control Objective 1-1; Cross-Habitat Oil Spills Prevention Action 

1-3-5; and Chapter 10: Subtidal-Wetland Design Integration Restoration 

Action 3-1-2.)
 147

CHAPTER TEN 

Integrated Restoration 

Together with the baylands ecosystem Habitat Goals Project 

and the Uplands Habitat Goals Project (see box below), the Subtidal 

Goals Project represents a milestone in regional habitat planning for 

San Francisco Bay and its watersheds. We now have a comprehensive and 

innovative ecosystem-based management vision for a continuum of habitat 

types from the bottom of the bay to tidal wetlands and grassland transition 

zones to upland areas. Each goals report outlines recommendations for the 

preservation, restoration, and protection of habitat. These reports provide 

important tools to educate agencies, non-profits, private foundations, and 

others about the value of these habitats, and offer background information that 

can be used to seek funding for implementation. Although at present these 

three goals projects are proceeding independently of each other, there may be 

RELATED REGIONAL PLANNING EFFORTS 

Baylands Habitat Goals Project

The Baylands Ecosystem Habitat Goals Project, completed in 

1999, used available scientific knowledge to identify the types, 

amounts, and distribution of wetlands and related habitats 

needed to sustain diverse, healthy communities of fish and wildlife resources in the San Francisco Bay Area. It provided a biological basis for a regional wetlands planning process to assist public 

and private interests seeking to preserve and restore the ecological integrity of wetland communities. Remarkably successful 

at articulating a vision for protecting and restoring 100,000 acres 

of wetland habitat, its report informed stakeholders about the 

importance of wetland habitat and the need for future funding. 

By November 2010, more than 40,000 acres of tidal wetlands 

had been acquired for restoration by private, local, state, and 

federal partners. Many agencies and non-profit organizations 

have participated in implementing report recommendations. For 

example, the San Francisco Bay Joint Venture (SFBJV) is helping 

coordinate implementation of some recommendations with local, 

state, and federal partners, and has developed an Implementation 

Strategy based on the recommendations. With its partner database, the SFBJV has been tracking progress towards tidal wetland 

acquisition, planning, and restoration. The State Coastal Conservancy is currently planning an update to the Baylands Goals 

Report, to incorporate climate change considerations.

Uplands Habitat Goals Project

The San Francisco Bay Area Upland Habitat Goals Project has 

completed several reports over the past decade, with more 

underway, using a science-based process based on existing and 

new data supplemented by expert opinion to recommend the 

types, amounts, and distribution of upland habitats, linkages, 

compatible uses, and the ecological processes needed to sustain diverse and healthy communities of plant, fish, and wildlife 

resources in the Bay Area. 

The project’s objectives are to: 

1) increase the acreage of protected lands by increasing public 

and private funding for habitat acquisition and restoration; and 

2) develop an increased awareness of key habitats among land 

management agencies and local jurisdictions charged with land 

use planning. The GIS database and reference documents developed by this project are intended to be decision-support tools 

to inform voluntary, non-regulatory investments, protection 

strategies, and management policies of public resource agencies, 

nonprofit conservation organizations, local government, legislators and private foundations seeking to preserve, enhance, and 

restore the biological diversity of upland habitats before development eliminates remaining opportunities.
148 • San Francisco Bay Subtidal Habitat Goals Report

benefits to linking restoration projects in subtidal habitats to those in adjacent 

marshes and uplands. These benefits arise from landscape-scale ecological 

processes, i.e., processes that extend over more than one habitat type. For 

example, restoration at a nearshore subtidal site may enhance sediment 

retention that would favor persistence of an adjacent marsh.

Carrying this further, it may also be possible to design restoration of subtidal 

habitats not only to protect and interact with marshes and uplands, but also as 

a substitute for or a complement to seawalls and breakwaters used to protect 

vulnerable shorelines. With rising sea level (Appendix 2-2) and ongoing loss of 

sediment (Chapter 4), the value of shoreline protection and the consequences 

of erosion at unprotected shorelines become more apparent. 

An Integrated Habitat Approach to Restoration 

Most of the habitat restoration projects implemented in and around San 

Francisco Bay in the last 40 years have focused on single habitat types such 

as marshes and riparian zones. A few large regional restoration projects have 

incorporated planning for multiple habitats across landscapes, including the 

South Bay Salt Pond Restoration Project and the Dutch Slough Restoration 

Project. Integrating restoration between subtidal and nearby marsh and upland 

habitats may provide ecological benefits, as discussed below, and the resulting 

interactions may result in cost savings compared to equivalent isolated restoration projects.

Many ecosystem processes occur at a larger scale than individual habitats. 

These processes include:

•	 Sediment transport and retention (Appendix 2-1, sediment narrative) at 

nested scales: sediment supply and loss occur at the scale of the estuary; 

the major estuarine basins have water circulation cells that cause them 

The San Francisco Bay shoreline has 

multiple habitat types: sand, cobble, 

and open water.
Chapter Ten: Integrated Restoration • 149

to gain or lose sediment somewhat independently of each other; within 

these basins are regions where sediments accumulate or are eroded over 

seasonal or longer periods; and at smaller scales, marshes exchange sediment with nearby shallow subtidal regions. 

•	 Biogeochemical processing of materials: marshes are sites of transformation of substances between alternative chemical forms. These substances 

may enter a marsh from the adjacent waters in one form, become transformed, and leave the marsh in a different form. This can affect nutrient availability, oxygen supply, and the availability of organic carbon to 

microbes both within the marsh and in nearby waters.

•	 Net organic production: marshes produce vast amounts of organic 

carbon. The importance of this carbon to the food webs of adjacent 

waters has been debated for decades. The magnitude and direction of 

movement of organic carbon between marshes and adjacent waters, and 

the forms (living and non-living) and degree of bioavailability of this 

carbon, likely vary with the physical configuration of the site, biological 

components, season, and freshwater flow patterns (Dame et al. 1986). 

The key point, though, is that there are strong links between marshes and 

adjacent waters.

•	 Movement of organisms: mobile estuarine organisms including birds, 

fish, and shrimp move into marsh channels and onto marsh plains, feeding there and moving living biomass from the marsh to the open water. 

This process may be an important mechanism for exporting high marsh 

productivity to the open water in a form that is usable to higher organisms (Kneib 1997). Taken more broadly, movement of organisms links 

marshes and adjacent subtidal habitats with the major rivers feeding the 

bay (anadromous fish), a large swath of the Pacific Ocean (anadromous 

salmon), and the Canadian and Alaskan Arctic (migratory birds).

Subtidal eelgrass bed offshore from an 

intertidal rocky shoreline.
150 • San Francisco Bay Subtidal Habitat Goals Report

Restoration can be expensive, uncertain, and difficult; therefore it seems logical to design restoration projects to capitalize on links between nearby habitats. 

Subtidal habitats that increase bottom friction, mainly oyster reefs and eelgrass 

beds, could be placed so as to attenuate wind waves and thereby buffer tidal 

wetlands and creek mouths from erosion. The combination of marsh restoration and nearshore subtidal habitat restoration could create local zones of 

sediment retention, minimizing the need for ongoing intervention. Local concentrations of oysters on constructed reefs may increase water clarity, thereby 

increasing the amount of light available to nearby eelgrass beds.

An additional advantage of integrated restoration is to reduce the effects of 

habitat fragmentation. Extant marshes are small and geographically dispersed. 

Even after completion of the Baylands Goals Project, these habitats will not 

approach the extent and contiguity of pre-settlement marshes. Yet, connectivity 

among habitat elements is a key feature of ecological landscapes, where subsidies of nutrients, other substances, or organisms can cross habitat boundaries 

and enhance overall productivity (Polis et al. 1997). Although the magnitude 

of this enhancement would be difficult to measure at an integrated restoration site, the existence of these known links and the conceptual importance of 

subsidies and flows between habitats supports the integration of subtidal and 

marsh or riparian restoration. Integration may also help foster upslope migration of the marsh as sea level rises at some locations. Since this movement will 

require additional sediment, having an adjacent subtidal source or retention 

area for sediment may help the marsh grow at its upland edge.

Although integrated restoration seems promising, present knowledge is inadequate to design projects that will achieve the goals of this chapter. As with 

restoration of individual habitats, this suggests using an adaptive, phased 

approach in which learning at each phase provides input to decisions about the 

scale, scope, and design at the next phase. 

Figure 10-1: Conceptual cross-section of a living shoreline design.
Chapter Ten: Integrated Restoration • 151

Living Shorelines: Softening and Protecting Edges

People are likely to adapt to sea level rise and a decrease in sediment supply 

by increasing the height and extent of levees and seawalls to protect their 

property. These actions have consequences beyond the property boundaries. 

For example, seawalls reflect incoming wave energy, whereas a natural, gradually sloping shore absorbs and dissipates the energy (see also Chapter 6). The 

reflected wave energy is thereby available to erode unprotected shorelines 

elsewhere. As the degree of armoring increases, erosion of remaining unprotected shores is likely to increase. Furthermore, enhanced erosion immediately 

offshore from the armored shoreline realigns the distribution of sediments, 

which can result in unintended deposition in remote areas. These widespread 

consequences, such as transfer of deposition or erosion to other areas, represent an externality to the cost of the shoreline protection—a cost not borne by 

the property owner.

Although these effects have been known for a long time, alternative methods 

for protection of vulnerable shorelines have been slow in coming. A recent 

National Research Council publication on shoreline protection (NRC 2007) 

examines current practices for minimizing erosion and concludes with a call for 

alternative approaches at project to regional scales. They acknowledge that specific effects of hard structures on unprotected areas can be difficult to quantify:

In most areas, the scope and accessibility of information regarding the 

causes of erosion at specific sites and the overall patterns of erosion, accretion, and inundation in the broader region (estuary, lagoon, littoral cell) 

[are] insufficient to support the development of an integrated plan for managing shore erosion. (NRC 2007, Executive Summary)

The NRC report nevertheless recommends alternative approaches including 

the use of soft structures and incorporation of living materials into shoreline 

protection schemes. These schemes can be characterized as “living shorelines” 

(Erdle et al. 2008; see also http://www.habitat.noaa.gov/restoration/techniques/

livingshorelines.html) that can 1) protect adjacent vulnerable shorelines; 

2) minimize externalities such as the transfer of erosion; and 3) increase the 

extent of potentially valuable subtidal habitat (see Chapters 7 and 8 for a discussion of the potential value of these habitats).

The idea that living materials can help protect shorelines is not new, as there 

are many examples of shoreline protection by naturally-occurring barriers (see 

sidebar). However, the use of natural materials in restoration, construction, or 

enhancement of shorelines for protection of vulnerable areas is not yet widespread (see, for example, Williams and Thom 2001). Reasons for this include 

tradition, perceptions (or reality) of high cost, and lack of knowledge necessary 

to design such structures (NRC 2007). In the meantime, however, integrated 

living shoreline projects have been successfully tested by NOAA’s Communitybased Restoration Program, US Fish and Wildlife Service’s Coastal Program, 

Chesapeake Bay Foundation, North Carolina Coastal Federation, North 

Nature’s living

shorelines

Nature provides many examples 

of shorelines protected by 

living habitats. The most obvious 

example is coral reefs. Reefs grow 

in all tropical oceans, and typically 

consist of a massive, rocky bed 

of limestone from previous reef 

development, and a crown comprising corals and coralline algae 

in a strong, wave-resistant matrix. 

Two elements of a coral reef are 

essential for its function in shoreline protection. First, the coral/

algae matrix grows to approximately mean sea level, maintaining 

a barrier to waves. Second, the 

surface of the reef is rough at all 

spatial scales, maximizing friction 

and extracting most of the energy 

from waves.

The protective value of coral 

reefs can be seen most clearly 

on atolls, where human populations can survive on land that 

is at most a few meters above 

sea level. Even during hurricanes, 

overtopping of atolls by wind 

waves is surprisingly uncommon 

(although this may change with 

sea-level rise). Low-lying areas of 

high islands and mainlands can 

also be protected by fringing or 

barrier reefs.

Other examples of natural shorelines that inhibit erosion (or even 

trap sediments) include mangrove 

swamps, extensive tidal marshes, 

and river deltas.
152 • San Francisco Bay Subtidal Habitat Goals Report

This degraded shoreline edge could 

be improved using integrated habitat 

restoration techniques.

A healthy shoreline edge with oysters 

and seaweed.

Carolina Division of Coastal Resources, Florida Department of Environmental 

Protection, and other funding and restoration partners for more than two 

decades on the East Coast and areas of the Gulf Coast (Erdle et al. 2008).

The interest in restoration of oyster and eelgrass beds and the need for increasing shoreline protection in San Francisco Bay present an opportunity for 

beginning experimental work at the pilot project scale to design living shorelines. However, both the quantitative effects of hard structures (and therefore 

the magnitude of externalities in relation to the cost of the structures) and the 

best design practices for minimizing these effects are poorly known. As with 

restoration of oyster and eelgrass beds and integrated shorelines, this implies a 

need for a careful, phased approach using an adaptive management framework 

(Chapter 2) to ensure that fundamental questions about benefits and design 

can be answered early, and knowledge gained in early phases can improve 

practices and outcomes in later phases.

Examples of Living Shoreline Pilot Projects 

that Could be Attempted in San Francisco Bay

Living shorelines represent a new approach to shoreline stabilization. Yet 

knowledge of their benefits and best practices is scanty and is specific to locations other than San Francisco Bay. This suggests that we develop and test small 

pilot projects at sites vulnerable to erosion. These projects would test the use 

of biological treatments in place of hard structures, and test new or modified 

structures made of materials and in locations that may provide expanded habitat benefits. Many permitting and regulatory issues must be addressed as these 

pilot projects move forward, including issues of site suitability, material suitability, risk assessment, effectiveness of scale, habitat conversion and mitigation, and potential conflicts in protecting newly created habitat and structures 

that require ongoing, long-term maintenance.

Coral reefs are one type of living 

shoreline.
Chapter Ten: Integrated Restoration • 153

Classes of projects that could be attempted at the pilot scale include the 

following:

Living breakwaters are structures placed parallel to the shore in mediumto high-energy open-water environments to dissipate wave energy while 

providing habitat and erosion control benefits to an ecosystem. These 

breakwaters are constructed of native rock or artificial reef structures seeded 

with oyster spat. Quiescent areas between the breakwaters and the shoreline 

could be planted with SAV and marsh grasses to create intertidal and marsh 

habitat for aquatic organisms.

Living seawalls incorporate subtidal habitat into structures built for the primary 

purpose of protecting shorelines. For example, a recent experiment in Seattle 

installed panels along a seawall with various shapes and textures to determine 

rates of colonization by marine flora and fauna. Troughs were also installed 

extending out from the face of the seawall to mimic shallow water habitats that 

have largely been lost along the Seattle shoreline. The potential benefits could 

include greater nearshore productivity and trapping of sediment and organic 

matter. (http://www.cityofseattle.net/Transportation/seawall.htm)

Living docks are exemplified by a project in West Palm Beach, Florida. The 

dock is designed to support natural systems such as mangroves, grasses, and 

oysters that create habitat and provide water-filtration services. The living dock 

system is multi-layered and includes geotextiles enclosing a special soil mix 

for floating mangroves and marsh plants. Embedded within the geotextile 

layers are oyster shells from restaurants, which were placed to help spur natural 

oyster growth.

Oyster balls made of concrete and shell can be used at living shoreline sites to 

decrease wave energy while enhancing fish and oyster habitat. These structures 

can dissipate wave energy, decreasing coastal erosion and providing a reducedenergy area behind them in which newly planted vegetation can grow. As discussed in Chapter 7, key research questions need to be answered as to the benefits of the reef structures themselves versus the benefits from the settled oysters. Top: Volunteers plant a living shoreline.

Center: The Seattle Seawall tests 

various substrate types and 

orientations to identify which provide 

the best habitat for subtidal species.

Bottom: A living dock in Florida uses 

Virginia oysters to filter the water.

Biologists and volunteers deploy a 

Reef BallTM that will attract native 

oysters.
154 • San Francisco Bay Subtidal Habitat Goals Report

Submerged aquatic vegetation such as eelgrass dampens wave energy, stabilizes 

nearshore sediments, improves water quality via nutrient uptake, and provides 

food and shelter for other marine organisms (Chapter 8). When these are used 

in conjunction with other living shoreline components such as marsh grasses, a 

natural shoreline buffer may be created that reduces coastal erosion and stabilizes sediments via root growth. 

Intertidal sand beach or subtidal sand habitat is included in this discussion as an 

alternative to hard shorelines, although the principal function arises through 

geophysical rather than biological processes. Beaches and marsh berms bordering tidal marshes provide the first line of dynamic defense against wind-wave 

erosion during extreme high tides and storms. Nourishment of erosion-prone 

marsh scarps or berms with sand, gravel, or shell is likely to provide or lead 

to erosion buffering, shorebird refuge, and vegetation cover, and to approximate long-lost connections between beach and marsh (Baye 2007). A few pilot 

projects to replenish sand beaches have been conducted in San Francisco Bay, 

including at Coyote Beach in San Mateo and Pier 98 in San Francisco. Future 

projects could be designed with more specific focus on sand transport pathways and the benefits and impacts to the adjacent offshore subtidal areas. 

Tidal wetlands include subtidal sloughs and channels that connect to offshore subtidal habitats.

A sand beach restoration project 

at San Francisco, south end of 

Pier 94, three months postnourishment (2006).
Chapter Ten: Integrated Restoration • 155

A healthy tidal marsh includes many 

subtidal channel edges.

Enhanced intertidal or subtidal rocky habitat.The extent of natural rock is limited to a few areas mainly in central San Francisco Bay (Chapter 5). Some rock 

has been placed into artificial configurations at sites such as Albany Beach. 

Opportunities exist to reuse and reconfigure existing native rock at sites where 

shoreline restoration is being planned and at tidal elevations that maximize 

colonization by native flora and fauna.

Rationale for Establishing Goals for Subtidal-Wetland Integration

In contrast to the habitats discussed in Chapters 4-9, the decision tree (Chapter 

2) provides no guidance for integrating subtidal habitats with marshes and 

riparian habitats or for establishing living shorelines. However, the high degree 

of uncertainty, even about appropriate methods to conduct pilot projects under 

these topics, requires the application of adaptive management principles for 

these pilot projects to be most effective.

Goals for integration generally focus on pilot-scale projects to test concepts and 

practices at a large enough scale to be meaningful. This contrasts with the shellfish and SAV chapters (7 and 8), which call for a phased approach that moves 

beyond pilot projects once the requisite knowledge has been developed. Here 

the degree of uncertainty about the success of integrated restoration is sufficient to preclude planning for larger-scale projects until and unless the success 

of early pilot projects can be convincingly demonstrated.

The knowledge-gathering element of the pilot projects should focus in particular on the synergistic aspects of integrated restoration. That is, restoration of a 

particular habitat type (for example eelgrass) is assumed to proceed under an 

adaptive framework in which an explicitly designed process gathers knowledge 

about the ecosystem benefits of and best practices for restoring that habitat. In 

integrated restoration additional information must be gathered on the extent to 

which this restoration project achieves goals that cross habitat boundaries, such 

as enhancing connectivity with marshes or protecting vulnerable shorelines.

As with habitat-specific restoration, the degree of uncertainty about integrated 

restoration suggests that pilot projects lacking the full adaptive management 

framework will fail to provide the knowledge needed to proceed beyond the pilot stage. The only possible justification for 

conducting pilot projects, which are intended eventually to 

lead to larger-scale projects, is to develop the knowledge to 

determine whether a shift to a larger scale is warranted. This 

gives strong justification to a recommendation not to undertake such projects without the requisite pre-project analyses, 

monitoring and investigations during and after construction, 

and post-project analysis.

Goals in this chapter could be refined by the introduction of 

expertise from places where these approaches have been tried. 
156 • San Francisco Bay Subtidal Habitat Goals Report

Marshes are eroding around the 

bay’s edges.

Therefore a valuable initial step is to host a workshop on these approaches. 

Invited participants from other locations in the U.S. and overseas would be 

asked to present a summary of their findings, and local participants would 

provide some context on current conditions and challenges. The final step in 

such a workshop would be to develop a set of recommendations specific to 

San Francisco Bay.

The specific restoration actions and sites listed below include considerations such as: (1) presence of and knowledge of existing subtidal resources; 

(2) presence of current pilot subtidal restoration projects that could be 

expanded; (3) proximity of subtidal resources to wetland restoration sites 

recommended by the Baylands Habitat Goals Project; and (4) for living 

shorelines, proximity to areas of current or anticipated shoreline erosion. 

Research goals focus first on the overall benefits of integration, and secondarily on further developing site criteria and best techniques for living shoreline designs and monitoring.

Science Goals for Subtidal-Wetland Integration

Subtidal-Wetland Design Integration Science Goal 1 

Understand the ecosystem services supported by marshsubtidal integration and living shorelines, and in what quantities.

Question A. What quantitative synergies in ecosystem services arise when subtidal habitats are linked to marshes and riparian areas?

The basic question of which ecosystem services are provided by the individual 

habitats is addressed in each of the habitat chapters. Is it possible to measure 

the additional benefits of locating habitat restoration sites adjacent to wetlands? 

Are there disadvantages, and do the benefits of such location outweigh other 

criteria for site selection?

Question B. Which ecosystem services are provided by living shorelines, and in 

what amounts?

This question should be addressed repeatedly throughout the adaptive management process for living shorelines.

Subtidal-Wetland Design Integration Science Goal 2 

Develop best practices for integrating subtidal restoration 

with adjacent wetlands.

Question A. What characteristics of shorelines lend themselves to cross-shore 

integration?

Question B. Which wetland sites are likely to be most vulnerable to long-term 

changes in sea level and sediment supply?
Chapter Ten: Integrated Restoration • 157

Investments in tidal wetland 

restoration projects need to be 

protected in the face of climate 

change and other future changes to 

the bay.

Many habitat types can occur at 

the same location: eelgrass, native 

oysters, and macroalgal beds.

Question C. Which approaches result in the most effective and persistent wetlandsubtidal restoration projects?

Subtidal-Wetland Design Integration Science Goal 3 

Develop best practices for pilot projects to create living 

shorelines.

Question A. What criteria should be used to choose locations for living shorelines? 

Question B. How does the physical configuration of a living shoreline influence 

its ability to protect inshore areas, and what are its ancillary effects on other 

habitats?

Relatively little is available in the scientific literature on the design and construction of living shorelines, although outreach programs on these topics are 

available at several universities, and NOAA has funded several projects. Most 

of these efforts are on the East and Gulf coasts. While some lessons from these 

projects will be applicable in the bay, several important differences (for example in tidal range, sediment characteristics, plant types) may affect the performance of different designs.

Question C. How self-sustaining are the alternative designs?

The ideal design would result in living shorelines that are self-sustaining or 

require minimal human intervention. Some periodic maintenance may be 

needed, such as cleaning shell reefs or placing clean dredged sediment to provide a source of sediment to maintain habitats.
158 • San Francisco Bay Subtidal Habitat Goals Report

Restoration Goals for Subtidal-Wetland Integration

Subtidal-Wetland Design Integration

Restoration Goal 1 

Explore the integration of upland, intertidal, and subtidal 

habitats in San Francisco Bay.

•	 Subtidal-Wetland Design Integration Restoration Objective 1-1: Select 

sites that have the greatest opportunities for integrating subtidal habitat with 

other restored or important habitats for pilot subtidal restoration projects 

near locations identified by the San Francisco Baylands Ecosystem Habitat 

Goals Project. 

Possible locations include: 

•	 San Pablo Bay: study potential resources and restoration activities in areas 

offshore from Sears Point, San Pablo Bay National Wildlife Refuge and 

Tubbs Island, and other restoration sites.

•	 Corte Madera area: Muzzi Marsh, Corte Madera Ecological Reserve, 

Heard Marsh: existing wetlands and restored eelgrass, link to living shoreline project 

•	 Richardson Bay: wetland restoration linked to existing oyster/eelgrass 

populations

•	 Breuner Marsh and Point Molate: link to Point San Pablo eelgrass bed

•	 Eastshore State Park: wetland restoration linked with oyster and eelgrass 

restoration, creek daylighting

•	 Central and North Bay Islands: link rocky habitat with eelgrass and 

oyster beds

•	 South Bay Salt Pond sites; Eden Landing and other sites: link to southernmost eelgrass population, native oyster restoration

•	 Subtidal-Wetland Design Integration Restoration Objective 1-2: 

Support and promote integration of subtidal habitat design and subtidal 

enhancement, restoration, and monitoring into tidal wetland restoration 

projects around the bay.

Subtidal-Wetland Design Integration Restoration Action 1-2-1: At appropriate 

sites, incorporate project elevations that include gradual slopes across a 

range of depths, linking the shoreline edge to shallow and deep waters, and 

allowing for a variety of topography and micro-habitats to benefit multiple 

species. Some sites, such as rocky headlands with naturally steep slopes, 

would not be appropriate for this treatment.

Subtidal-Wetland Design Integration Restoration Action 1-2-2: Incorporate a 

variety of subtidal channel configurations into tidal wetland restoration. 
Chapter Ten: Integrated Restoration • 159

A typical salt pond levee with 

compacted soil covered in invasive 

crystalline iceplant. There are many 

opportunities to test new multihabitat restoration approaches within 

the South Bay Salt Pond Project.

Subtidal-Wetland Design Integration Restoration Action 1-2-3: Reduce or modify 

hard artificial structures within restoration sites to protect and improve 

subtidal channel habitat functions. See Artificial Structures Protection 

Goals, Chapter 6.

Subtidal-Wetland Design Integration Restoration Action 1-2-4: Design tidal 

wetland restoration projects to better enhance and improve transition (edge) 

zones between tidal and subtidal habitat, and include multiple arrays of 

small habitat types (such as eelgrass beds, native oyster beds, kelp and algal 

fringes, rocky intertidal, and intertidal sandy beaches).

Subtidal-Wetland Design Integration Restoration Objective 1-3: Increase 

regional coordination and collaborative planning to advance subtidal-wetland 

integration.

Subtidal-Wetland Design Integration

Restoration Goal 2 

Integrate habitat flexibility to increase resilience in the face of 

long-term change at habitat restoration sites around the bay. 

•	 Subtidal-Wetland Design Integration Restoration Objective 2-1: 

Design habitat restoration projects to account for long-term changes 

including sea level rise and loss of sediment, by increasing resiliency of 

existing habitat types and facilitating upslope habitat migration.

Subtidal-Wetland Design Integration Restoration Action 2-1-1: Design projects to 

include subtidal habitats and natural bioengineering techniques that buffer 

wave action and increase sediment deposition to minimize shoreline and 

wetland erosion.

Subtidal-Wetland Design Integration Restoration Action 2-1-2: Integrate natural 

sedimentation processes into restoration designs to capture sediments and 

minimize erosion. For example:

•	 Avoid siting restoration projects or breach locations in highly erosional 

areas.
160 • San Francisco Bay Subtidal Habitat Goals Report

•	 Develop designs that maximize depositional areas and integrate local 

creek mouths.

•	 Promote use of clean locally-dredged sediment to supplement sediment 

where appropriate.

•	 Design gradual slopes that slow wave action and reduce erosion.

•	 Use bioengineering techniques such as eelgrass plantings and rock or 

oyster shell to stabilize sediment.

Subtidal-Wetland Design Integration Restoration Action 2-1-3: Monitor and 

evaluate existing subtidal resources and habitat types to track impacts of sea 

level rise to subtidal habitats that occur within and adjacent to selected tidal 

wetland restoration projects.

Subtidal-Wetland Design Integration

Restoration Goal 3 

Explore the use of living shoreline projects as a way to achieve 

multiple benefits in future shoreline restoration.

•	 Subtidal-Wetland Design Integration Restoration Objective 3-1: 

Evaluate living shoreline and associated techniques outlined above by 

implementing five small-scale pilot projects in San Francisco Bay by 2015.

Potential living shorelines sites:

•	 Corte Madera Bay, Corte Madera

•	 Eastshore State Park, multiple sites

•	 South Bay Salt Pond Project (Eden Landing Ecological Reserve, Alviso 

Pond Complex, Ravenswood Pond Complex)

•	 Albany Beach, Albany

•	 Breuner Marsh, Richmond

•	 Crown Beach, Alameda

•	 Former Naval Air Base lands, Alameda

•	 Hunters Point and Yosemite Slough areas, San Francisco

•	 Arambaru Island, Tiburon

•	 Sears Point, San Pablo Bay National Wildlife Refuge

•	 Suisun Marsh

(See Figure 4-5, Chapter 4: Map of suggested locations for pilot intertidal sand 

beach enhancement and living shorelines).

Subtidal-Wetland Design Integration Restoration Action 3-1-1: Incorporate 

multiple habitat types into pilot living shoreline designs; test effectiveness 
Chapter Ten: Integrated Restoration • 161

Eelgrass restoration can be 

integrated into rocky intertidal 

shorelines or tidal wetlands.

at buffering wave action, stabilizing sediments, and providing habitat; and 

evaluate success of restoration techniques and materials, including:

•	 soft substrates (mudflat, shell hash, sand)

•	 native rock and cobbles, stone, stone sills

•	 artificial structures (reef balls, reef blocks, etc.)

•	 native oyster and mussel treatments

•	 native eelgrass treatments

•	 native macroalgal treatments

Subtidal-Wetland Design Integration Restoration Action 3-1-2: Incorporate living 

shoreline techniques to retain mud and sand from natural deposition or 

from sand replenishment activities.

•	 Subtidal-Wetland Design Integration Restoration Objective 3-2: 

If small pilot projects prove successful at achieving the three purposes 

discussed above, expand small-scale projects or implement 10 mid-scale 

living shoreline and living breakwater projects in San Francisco Bay by 2020.

•	 Subtidal-Wetland Design Integration Restoration Objective 3-3:

Pending the results of evaluations of pilot-scale studies, incorporate living 

shoreline components and naturalized habitat into the design of new and 

replacement shoreline protection structures.

 163

CHAPTER ELEVEN

 Implementation 

T his report makes recommendations for protecting and 

improving subtidal habitat in the estuary. As stated previously, the 

recommendations are not proposed regulatory changes. However, 

actions could be taken by appropriate agencies in the future to further improve 

subtidal habitat through their own regulatory processes. The background 

information and associated goals in this report are designed to help resource 

agencies and other organizations implement subtidal habitat development, restoration, or enhancement projects. This information can be used in designing 

research, taking management actions, implementing protection strategies or 

restoration projects, or updating existing laws and policies. Agencies and other 

organizations can also use the document and associated goals to raise funds for 

scientific research and restoration projects. 

To implement the subtidal goals at a broader level, agencies and other organizations may use this document to develop or modify their policies based on 

the goals presented herein. Any policy modification or policy development will 

entail a separate process in which an individual agency will need to analyze the 

recommendations in the context of their existing authorities and mandates.
﻿164 • San Francisco Bay Subtidal Habitat Goals Report

Regulatory Agencies’ Roles

Several agencies regulate activities within the subtidal area of the bay. Some are 

focused on species protection, fisheries management, or water quality. Others 

have a broader habitat focus, while others must balance ecosystem and development needs. In reviewing these goals, some agencies may decide to take 

regulatory action through their existing authorities or to expand their current 

authorities through legislation or regulation changes. In either case, agencies 

must utilize existing public rule making processes. The following discussion 

describes and lists potential actions that agencies with regulatory authority may 

consider implementing to protect subtidal habitats.

While these regulatory measures would likely reduce impacts to the subtidal 

habitats, as set forth in previous chapters, more research about these habitats is 

needed. As research is completed to better understand the functions and ecosystem services of subtidal habitats, information gained should directly inform 

management actions such as those listed below. In the interim, the Subtidal 

Goals Project recommends using a precautionary approach in managing subtidal habitats.

Examples of Potential New Regulatory Guidance

Benthic disturbance: 

Benthic disturbance can occur in many forms. Blasting, dredging, and sand 

mining literally remove the substrate on or in which organisms live. Placing new structures, be they pier pilings, floating docks, outfalls, or pipelines, 

also eliminates the surface, and in some cases, subsurface in which organisms 

live. Similarly, mechanical destruction from anchors and mooring devices 

can impact aquatic vegetation. Because dredging, sand mining, and placing 

Creosote pilings provide space for

organisms to attach to but may also

release toxins into bay waters.
Chapter Eleven: Implementation • 165

structures are the most widespread human activities that disturb the subtidal 

bottom to the degree of actually removing habitat, limiting these activities 

would protect subtidal habitats. 

•	 Avoid new dredging, sand mining activities or removal of native rock 

from the bay, especially in areas with aquatic vegetation or high density 

shellfish beds.

•	 Avoid locating projects that include or may require dredging in areas of 

high sedimentation.

•	 Avoid placing structures in subtidal or intertidal areas of the bay, 

especially in areas with or adjacent to eelgrass, aquatic vegetation, or 

shellfish beds.

Benthic disturbance: damage to habitat

Subtidal habitat can also be impacted from loss of light penetration and 

extended periods of turbidity and high suspended sediment loads. Potential 

regulatory considerations for activities that create these types of impacts (i.e., 

dredging, vessel propeller wash, and placing structures) could be improved by 

the following regulatory considerations. 

•	 Remove illegal structures, including mooring facilities, from areas with 

submerged aquatic vegetation. 

•	 Locate proposed structures, including ferry terminals, away from areas 

with submerged aquatic vegetation, particularly eelgrass.

•	 Avoid anchoring barges in areas of submerged aquatic vegetation.

•	 Create no wake zones for vessels within 150 feet of submerged aquatic 

vegetation. 

•	 Locate ferry routes a minimum of 150 feet from submerged aquatic 

vegetation.

•	 Avoid new dredging projects within 150 feet of submerged aquatic 

vegetation.

Implementation Approach: Adaptive Management

As discussed in Chapter 2, the Subtidal Goals Project advocates an adaptive 

management approach to implementation both at project-specific and overall 

program levels. Although it is not perfect, adaptive management is probably 

the best way to increase knowledge of the functions and values of the habitats 

the Subtidal Goals Project purports to protect and to evaluate the success of the 

Subtidal Goals Project itself.

Applying adaptive management would represent a serious commitment on 

the part of the Subtidal Goals Project. Implementing adaptive management 

at the project scale would require that the adaptive process (Figure 2-3) be 
﻿166 • San Francisco Bay Subtidal Habitat Goals Report

designed into, and required as part of, any project to restore or enhance subtidal 

habitats. The value of knowledge must be seen as equivalent to the value of the 

actions themselves, given the level of uncertainty about the value of the actions. 

Requirements for project implementation would include conceptual and simulation modeling, predictions of outcomes, performance measures, a specific 

research and monitoring plan to evaluate progress and ecosystem response 

before and for some time after project completion, and a mechanism for reporting and, more importantly, responding to results as they become available.

In contrast to the project level, adaptive management can be implemented at 

the program level only if an institutional framework can be established that has 

the resources to do it. This will require a large-scale, long-term view and substantial budget both for the actions (including project-level adaptive management) and at the program level for the process of evaluation and revision.

Establishing a San Francisco Bay Subtidal Habitat Forum 

Consistent and enduring support for implementing the Subtidal Goals Project 

from individual agencies may be difficult to secure given political changes, staff 

turnover, budget fluctuations, and shifts in priorities. Successful implementation of the goals will require an entity or entities charged with raising funds 

and overseeing the realization of the goals in this document and the process of 

adaptive management necessary to realize the ecosystem benefits envisioned by 

this program. Implementation will require organizing stakeholders, identifying 

private owners of subtidal parcels, monitoring and tracking restoration projects, 

reviewing and reporting on knowledge gained and on progress in implementing 

the goals, revising the goals as needed, and educating the public about subtidal 

habitat in the estuary. This implementing entity might be an existing organization, a collaborative partnership among several agencies, or a new entity (such as 

a Joint Powers Authority or special district) created for this purpose.

The Subtidal Goals Project recommends that the lead entity (or entities) establish a Bay Area Subtidal Habitat Forum (Forum) to engage a broad network of 

agencies and partners who will participate in implementing subtidal habitat 

research, protection, and restoration goals. This Forum, made up of local, state, 

and federal agencies, academic institutions, non-profits, businesses, and industry, would increase regional coordination, collaborative planning and support 

for and awareness of subtidal protection and restoration. The Forum should be 

charged with leading adaptive management and making sure progress is being 

made towards the goals included in this document. 

Thoughtful planning must be put into the process by which the Forum is 

constituted, including how leadership is selected, which members should be 

included for participation and how they will be selected, which operating practices should be adopted, which agency staff resources will be provided, and 

what additional funding or resources are needed and where those resources 

will come from. 
Chapter Eleven: Implementation • 167

Existing successful regional partnerships can provide a model framework 

for developing the Forum. Several groups of agencies have enlisted the aid 

of experts and stakeholders to form advisory boards to establish long-term 

regional goals. It is important to look to these examples and build on lessons 

learned and draw on their experiences. Some successful examples of regional 

partnerships towards advancing vetted habitat goals include:

•	 San Francisco Bay Joint Venture: The Joint Venture brings together 

public and private agencies, conservation groups, development interests, 

and others to protect, restore, increase and enhance all types of wetlands, 

Public/Private Partnerships restoring subtidal habitat

A truck loaded with donated Pacific

oyster shell.

Native Oyster Restoration 

Projects: at the Marin Rod and Gun

Club and the Berkeley Marina. Several

innovative partnerships have been led

by Robert Abbott and Rena Obernolte

(Environ Corporation) and multiple

public and private partners, including

Drakes Bay Oyster Company (donated

clean Pacific oyster shell); Marin Rod

and Gun Club (provided permission and

access to use 30 acres of subtidal land);

Jerico Products (donated barge to help

with reef ball and shell pallet installation;

donated native mined shell for reef ball

mixture); and others.

Bair Island Sediment Task 

Force: The Bair Island Task Force is

a partnership between the Port of

Redwood City, the US Army Corps of

Engineers, US Fish andWildlife Service,

NOAA Fisheries, Bay Planning Coalition,

Save The Bay, San Mateo County Board

of Supervisors, the San Francisco

Bay Conservation and Development

Commission and others that has worked

to accomplish navigational dredging

at the Port of Redwood City and

the beneficial re-use of the dredged

sediment for habitat restoration at Inner

Bair Island.As a result, approximately

200,000 cubic yards of sediment were

pumped to Bair Island instead of being

dumped in the bay or ocean.This

contributed to the more-than 1 million

cubic yards of soil needed to raise the

elevation of Bair Island in preparation

for its eventual return to a tidal wetland.

At the same time, the dredging of the

channel at the Port of Redwood City is

crucial to ensure the ongoing economic

health of the Port and surrounding

businesses, and to maintain the Port’s

important contributions to the local and

regional economies.

Beneficial re-use of dredge material 

from the Port Of Oakland 50-Foot

Deepening Project: Oakland Harbor

is the second largest port on theWest

Coast and the fifth largest container

port in the nation.The federal channels

of the Oakland Harbor and Portmaintained berths were deepened

from 242 feet to depths of 250 feet.

Approximately 12.8 million cubic yards

of sediment were dredged for this

project and used to create eelgrass

beds and to enhance shallow water and

wetland habitats at the Middle Harbor

Enhancement Area, the Hamilton

Army AirfieldWetlands Restoration

project, and the MontezumaWetlands

Restoration project. Multiple partners

contributed to the planning of this effort,

including Port of Oakland, San Francisco

Bay Conservation and Development

Commission,Army Corps of Engineers,

Bay Planning Coalition, East Bay Regional

Park District, the California Coastal

Conservancy, and others.

A crane lifts Reef

BallsTM for placement

into offshore intertidal

and subtidal areas.

A boat is donated for restoring

oyster beds.
﻿168 • San Francisco Bay Subtidal Habitat Goals Report

riparian habitat, and associated uplands throughout the San Francisco 

Bay region to benefit birds, fish, and other wildlife. The diverse partners 

of the Joint Venture have been successful in advancing regional restoration projects, coordinating information about science and technical 

issues, and building collaborative partnerships for the benefit of multiple 

species and habitat types.

•	 Southern California Wetlands Recovery Project: The Wetlands Recovery Project (WRP) brings interested parties together to develop a coordinated, systematic, regional, and ecosystem-based approach to wetland 

protection. In 1997, with the execution of a Working Agreement, 19 

federal and state agencies developed an organizational framework and 

committed to designing and implementing a Regional Strategy for acquisition and restoration in order to increase the quantity and quality of the 

region’s wetlands. The long-term vision of the WRP is to reestablish a 

mosaic of functioning wetland and riparian systems that supports a diversity of fish and wildlife species. Projects completed since the WRP’s inception in 1997 have resulted in the acquisition of 6,603 acres, restoration 

or enhancement of 2,161 acres, and planning for 3,204 acres of wetlands. 

More than $500 million have been dedicated to WRP projects, including 

$330 million in state funds, $30 million in federal funds, and $147 million 

in local and private funds.

Ideas for Implementation

Lead entities for the Subtidal Goals Project or a Forum, if formed, should consider the following specific ideas for implementation:

•	 Pursue funding for agencies to provide staff support for and participation 

in the Forum and smaller topic-specific subcommittees. These smaller 

groups would also develop and share information that would inform 

adaptive management for future projects. 

•	 Identify opportunities to coordinate with ongoing federal, state, and local 

projects and programs. 

•	 Identify and develop funding mechanisms or initiatives that further study 

or promote subtidal habitat ecosystem services. Potential sources of funds 

include the NOAA Restoration Center or the State Coastal Conservancy; 

or mitigation funds associated with subtidal leases and project activities 

through the State Lands Commission or the San Francisco Bay Conservation and Development Commission.

•	 Apply adaptive management both at the program level, through funding 

opportunities, requirements and other mechanisms, and at the programmatic level, as an organizing principle for undertaking, assessing and 

modifying implementation, and for revising the goals (and this document) periodically, possibly integrating them with other goals projects. 

San Francisco Bay JointVenture
Chapter Eleven: Implementation • 169

•	 Develop specific indicators of successful implementation. The indicators 

should be both quantitative—such as acreage restored and number of 

goals implemented—as well as qualitative/contextual—such as changes 

in policies. Develop monitoring and data analysis programs to track indicators and evaluate success at both a project and regional scale and to 

measure changes at the institutional and ecosystem levels.

•	 Create or take advantage of an existing regional database and entity that 

would house, maintain, analyze, and provide access to monitoring data 

provided by the monitoring program described above.

•	 Increase communication and coordination with public and private 

subtidal landowners and provide information regarding the benefits of 

healthy subtidal habitat. 

•	 Develop a method to report on the program’s success in publications, on a 

web site, and at the State of the Estuary conference and other conferences.

Facilitate information exchange among managers and restoration practitioners across habitat types to increase opportunities for multi-habitat 

collaborative restoration projects and to minimize potential conflicts.

•	 Every 10 years, conduct a wholesale review and update of the goals and 

their implementation.

The Forum or other entities could also work to increase public awareness of 

and involvement in subtidal restoration. Ideas for outreach efforts include:

•	 Develop a web site to keep people informed of subtidal restoration projects and volunteer opportunities.

•	 Provide teaching materials that can be used in local schools or with local 

community-based volunteer groups; involve these groups in subtidal restoration and research projects.

•	 Use volunteers to help implement projects and raise awareness about the 

values of subtidal habitat. Partner with corporations, non-profits, social 

groups, and agencies to implement restoration and enhancement projects.

•	 Encourage or assist museums, aquariums, nature centers, and agencies 

undertaking restoration to include subtidal habitat interpretive informaVolunteers work tion in outdoor signs and indoor exhibits. to restore eelgrass.

Surf scoters over open water subtidal

habitats.
﻿170 • San Francisco Bay Subtidal Habitat Goals Report

•	 Encourage collaborations among local artists, seafood restaurants, nonprofits, and other venues to raise awareness about native oyster restoration projects.

•	 Create a shell-recycling program, based on standard protocols that have 

been developed to avoid disease and non-native species introductions, 

with local seafood restaurants to create a source of shell for restoration 

projects. (See Appendix 7-1).

Moving Forward

The Baylands Ecosystem Habitat Goals Project, the Uplands Habitat Goals 

Project, and the Subtidal Habitat Goals Project present an inspiring vision for 

what can be done to improve the condition of multiple habitat types around 

the bay, and the species that depend on them. Each project presents specific 

objectives and actions that can be tracked to help resource managers and others 

better understand the cumulative success of the implemented actions. Together, 

the three plans provide more information than has ever been available to 

resource managers and others engaged in ecosystem-based management and 

in-the-water/on-the-ground projects. The concerns regarding climate change 

and other long-term trends make these planning efforts even more timely and 

necessary for predicting, monitoring, and implementing adaptation measures 

to long-term changes in the San Francisco Bay watershed. If implemented, the 

three plans will conserve, protect, and restore important habitat for fish and 

wildlife, as well as the ecosystem services valued and relied on by humans.
 171

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Personal Communications

Chapter 2

Bruce Jaffe (USGS), 2010, to Marilyn Latta

Chapter 4

Janet Thompson (USGS), 2009, to Wim Kimmerer

Patrick Barnard (USGS), 2009 and 2010, to Wim Kimmerer
﻿178 • San Francisco Bay Subtidal Habitat Goals Report

Chapter 7

Robert Abbott (Environ), 2009, to Wim Kimmerer

J. Fuller, SFSU, 2010, to Wim Kimmerer

Chela Zabin (UC Davis), 2009, to Wim Kimmerer

Robert Abbott (Environ), 2009, to Wim Kimmerer

Robert Abbott (Environ), Chela Zabin (UC Davis), 2009, to Wim Kimmerer

Betsy Peabody (Puget Sound Restoration Fund), 2007, to Marilyn Latta

Jim Moore (CDFG), 2008, to Marilyn Latta 

Chapter 8

George Isaac (CDFG), 2010, to Marilyn Latta

Katharyn Boyer (SFSU), 2009, to Wim Kimmerer

John Takekawa (USGS), 2009, to Wim Kimmerer

Keith Merkel (Merkel and Associates), 2009, to Marilyn Latta

George Isaac (CDFG), 2010, to Korie Schaeffer

Chapter 9

Ryan Watanabe (CDFG), 2008, to Natalie Cosentino-Manning

Katharyn Boyer (SFSU), 2009 and 2010, to Wim Kimmerer
 179

photo and illustration credits

All photos and illustrations not in the public domain have been used by 

permission of the copyright holders. To obtain permission to use an image, 

please contact the credited entity directly.

Dennis Anderson Photography, www.bluewaterpictures.com: 

33, 53 (bottom), 81, 154 (top) 

Bay Conservation and Development Commission: 38, 49

Bay Conservation and Development Commission/Brenda Goeden: 8 (top left), 

12 (both), 59, 60 (both), 62

Peter Baye: 8 (top right), 63 (top), 65, 66, 70, 136 (both), 154 (bottom), 159

Bay Conservation and Development Commission/Dan Robinson, Former 

NOAA fellow: 29

California Academy of Sciences: S-14 (left), Dr. Antonio J. Ferreira © 

California Academy of Sciences: 1

California Department of Fish and Game/Jim Moore: 98 (top left, bottom 

right), 101 (top left) 

California Department of Fish and Game, Office of Spill Prevention and 

Response/Steve Hampton: 49

John Cloud, courtesy of Robin Grossinger, NOAA Central Library, San 

Francisco Estuary Institute: 30

Florida Department of Environmental Protection, Northwest District: 153 

(top)

Mike Greenfelder: 152

Gunther Graphics/Tim Gunther, www.gunthergraphics.biz: S-18–19 

Lorenz & Avelar, www.Lorenz-Avelar.com: cover; title; headers; exec summary 

S-1,S-2,S-3, S-4, S-6, S-7, S-8, S-9 (all), S-10 (bottom), S-11 (all), S-13, S-14 

(bottom), S-15, S-17 (top), S-20; 3, 16, 21, 32, 36 (top), 53 (left), 73, 75 (top), 

76, 79 (both), 80, 85 (bottom), 87 (all), 91, 93, 96, 115, 118 (both), 123, 135, 

138, 140, 141, 144, 145, 146, 149, 152 (top left, top right), 161, 163, 164, 170

Matt Manuel: 58

Marin Rod and Gun Club and Berkeley Marina native oyster restoration 

projects/Robert Abbott, Jerry McEwen, Rena Obernolte: 8 (center left, 

bottom left), 22 (both), 36 (bottom), 41, 52 (top left, center left), 89, 101 

(center left, bottom left), 102 (both), 104 (both), 108 (both), 109 (both), 110 

(bottom), 153 (bottom), 155, 167 (all)
﻿180 • San Francisco Bay Subtidal Habitat Goals Report

Marine Mammal Center: 59 (middle) 

National Oceanic and Atmospheric Administration(NOAA): 59 (top) 

National Park Service: 48 (all)

NOAA Fisheries, Habitat Conservation Division, Southwest Region/Charleen 

Gavette: 5, 10, 27, 54, 61, 71, 74, 77, 82, 94, 100, 113, 117, 119, 125, 139

NOAA Fisheries, Habitat Conservation Division, Southwest Region/Adrienne 

Harrison: 15

NOAA Restoration Center/Kevin Adams: 17 

Richardson Bay Audubon Center/ Suzanne Olyarnik: 42 (top), 133, 156, 157 

(top) 

San Francisco Bay Joint Venture: 168

San Francisco Boardsailing Association, www.SFBA.org: 40 (both)

San Francisco Estuary Invasive Spartina Project, State Coastal Conservancy: 

39 (right), 43 (both), 63 (bottom) 

San Francisco State University, Romberg-Tiburon Center for Environmental 

Studies/Wim Kimmerer: 17, 19, 22, 56, 78, 84, 97 (bottom left), 99, 121, 126, 

143 (bottom left) 

San Francisco State University, Romberg-Tiburon Center for Environmental 

Studies/Joanna York: 23 (bottom right)

San Francisco State University, Romberg-Tiburon Center for Environmental 

Studies/Katharyn Boyer’s lab: 4, 11, 18, 23 (left), 31, 97 (bottom), 98 (bottom 

left), 110, 111, 114, 127, 130, 131, 157 (left)

Seattle Department of Transportation: 153 (left center)

Michael Singer Studio (design), Tom Hurst (photo): 153 (bottom left)

Smithsonian Environmental Research Center and UC-Davis Romberg Tiburon 

Center/Chela Zabin: 44, 45, 143 (bottom) 

Steve Spiker, www.stealingbeautyphotography.com: 50

Jude Stalker: 42 (bottom), 51 (bottom), 52 (bottom), 169 (bottom) 

State Coastal Conservancy/Abe Doherty: 24, 25

State Coastal Conservancy/Marilyn Latta: 88 (both), 95 (bottom), 101 (top 

right), 137 (top), 148

UC Davis/Brian Cheng: S-10 (top left): 106, 107

USGS/Patrick Barnard, Bruce Jaffe, Susan de la Cruz: S-12, 28, 57, 69, 76, 85 

(top), 132, 169 (top) 

USGS/Cindy Brown: 39 (left)

Cleo Vilett, www.cleovilett.com: S-17 (bottom), 34, 55, 75 (bottom), 83, 95 

(top), 120, 142, 150

The Watershed Project/Chris Lee: 51 (top) 

David Wimpfheimer, www.calnaturalist.com: 122