The Science

The Feasibility of Wetlands Restoration by the San Francisco Bay Restoration Authority

James R. Hunt
January 28, 2016


Estuaries, where rivers meet oceans, are complicated by tides, seasonal freshwater input, the need for migratory aquatic species to pass through during various life stages, and the tendency of humans to settle in such environments for strategic, economic, and aesthetic reasons. All agree that the San Francisco Bay is a highly altered estuary through natural cycles of sea level fluctuations, massive debris from hydraulic mining activities, filling the Bay margins for trash disposal and creation of new land sometimes with toxic materials, altering freshwater inputs, and invasion by non-native species. Within this highly dynamic context, there is an awareness that the wetlands that previously ringed the Bay need to be restored because of their importance in estuarine ecology and as a component in mitigating some effects from ongoing sea level rise.

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Environmental protection is well established within the United States through local, state and national laws and resulting regulations. As problems with human health and ecological systems were identified by scientists and public interest groups, specific laws were passed, regulatory bodies were formed or had their scope expanded, and governmental infrastructures were created that managed the planning, design, implementation, and monitoring of various projects to restore and protect human health and ecosystem functioning. These institutions evolved out of relatively narrow focus areas such as drinking water, wastewater disposal, air quality from transportation and industrial sources, and solid waste management. Once many of the point sources of environmental degradation were identified and fixed, more difficult environmental problems remained that were not easily classified as an air, water or soil pollution problem, but represented an integrated response to multiple impacts such as experienced by San Francisco Bay. As a consequence of these more recently identified environmental challenges, narrowly focused regulatory agencies have had to broaden their scope and additional regulatory structures put in place to implement the public interest. Overlapping interests of regulatory agencies as well as public interest groups have led to an institutional complexity in part duplicating the environmental complexity found in San Francisco Bay.

San Francisco Bay Restoration Authority

The State of California formed the San Francisco Bay Restoration Authority to find funding for restoration activities within the San Francisco Bay area. Below is an attempt to summarize the history of the Authority and its current efforts to develop a local income stream from the nine Bay Area counties. Of specific interest is the methodology proposed for project selection, the oversight that will be provided, the required level of funding, the ability to assess projects, and the suitability of regulatory institutions to implement the intent of the legislation.

One likely origin of the San Francisco Bay Restoration Authority was a report by Save the Bay [2007]. The report advocated the investment of public funds to restore 36,000 additional acres of tidal wetlands around San Francisco Bay to achieve the 1999 vision of 100,000 restored acres [Goals Project, 1999].

Save the Bay estimated that at least $1.43 billion over 50 years would be required to restore the 36,000 acres as well as undertake monitoring and maintenance activities. Save the Bay recommended that the California Coastal Conservancy’s San Francisco Bay Area Conservancy Program serve as a special district to secure funding and develop priorities for allocating funds.

Rather than legislatively modify the Bay Coastal Conservancy Program to allow it to secure funding, the state passed legislation forming the San Francisco Bay Restoration Authority in 2008 with subsequent amendments []. The 2015 amendments established a debt limitation of 1.5 billion dollars and the repeal date for the Authority was extended to 2049. The Authority has a Governing Board composed of elected local representatives appointed by the Association of Bay Area Governments from county supervisors, elected city officials, and a representative from a regional park district. There was also an advisory committee composed of representatives from local governmental agencies and organizations representing environmental, labor, and business interests. As stated in the legislation: “It is in the public interest to create the San Francisco Bay Restoration Authority as a regional entity to generate and allocate resources for the protection and enhancement of tidal wetlands and other wildlife habitat in and surrounding the San Francisco Bay.” Eligible projects are required to do at least one of the following according to the legislation:
(1) Restore, protect, or enhance tidal wetlands, managed ponds, or natural habitats on the shoreline in the San Francisco Bay area, excluding the Delta primary zone.
(2) Build or enhance shoreline levees or other flood management features that are part of a project to restore, enhance, or protect tidal wetlands, managed ponds, or natural habitats.
(3) Provide or improve public access or recreational amenities that are part of a project to restore, enhance, or protect tidal wetlands, managed ponds, or natural habitats.
Grants awarded by Authority can be used for planning, construction, monitoring, operation, and maintenance. There was no mention of grants for research and there was no requirement for a scientific advisory board that could provide evaluation of proposed projects or assessment of project accomplishments.

The January 13, 2016 press release announcing the parcel tax to fund the Authority stated more broadly that shoreline projects would be funded that would protect and restore San Francisco Bay by:
(1) reducing trash, pollution and harmful toxins;
(2) improving water quality;
(3) restoring habitat for fish, birds and wildlife;
(4) protecting communities from floods; and
(5) increasing shoreline access for public enjoyment [].

The Authority has listed priorities for projects that are more generic such as benefitting the whole Bay Area, leveraging other resources, serving economically disadvantaged communities, work force development, incorporating monitoring and maintenance, and meeting the selection criteria of other Bay-focused agencies. The Authority has prepared a list and map of about 90 projects that they state are “Examples of projects anticipated to be eligible for Restoration Authority grants”. These possible projects do not include cost estimates or the number of acres of wetland being restored [].

The activities of Authority are done in coordinating with the San Francisco Bay Joint Venture, one of 18 federally funded Joint Ventures for North American Waterfowl Management. The Joint Venture has a local staff of 3 and a list of approximately 160 “Active Projects” in the Bay Area, many with a focus on San Francisco Bay but also include local watersheds as well as the Sacramento and San Joaquin Delta. This listing includes the number of acres for each project and the estimated funding needs for the next 3 to 5 years. Approximately 25% of the projects appearing on the Restoration Authority list also appear on the Joint Ventures list.

Through June 30, 2013 the Authority received and spent $250,000 to retain consultants to conduct surveys and provide legal and technical advice []. Save the Bay [2011] provided a Political Feasibility Analysis for passing a parcel tax in the 2014 general election. There are two additional presentations posted on the Authority’s website that provide analyses by consultants based on public opinion surveys on what it would take to pass ballot measures for restoration activities. Emphasis was on the type of tax (parcel, sales, or benefit assessment district), timing of the election, and what environmental message is most appealing to the voters. While “wetlands restoration” can improve “water quality”, the public has a more favorable opinion of the need for water quality improvements in the Bay and that message is recommended for public outreach efforts. The opinion surveys were probably funded by the Authority since there is no other evidence of what the Authority obtained for the $250,000 granted to it through ABAG.

As indicated previously, the Authority has decided to place a parcel tax of $12 on the June ballot.


There are two main problems with the actions being taken by the Authority to obtain revenue streams for wetlands restoration in San Francisco Bay. The first problem is that wetlands restoration will increase flood risk and this requires expensive mitigation measures. The parcel tax funds will need to cover these flood control expenses that are not separately identified compared to other activities. The second problem relates to the regulatory morass present within the Bay Area and the inefficiencies that result from a lack of coordination in permitting, monitoring, evaluation and data sharing. The science and management of wetlands restoration is not sufficiently developed to be able to efficiently manage the numerous projects the Authority has identified as potentially qualifying for funding.


The majority of the wetlands restoration work ongoing in the Bay Area involves breaching levees that isolated salt ponds, duck ponds, and agricultural land from tidal action. These lands have water surface elevations and land elevations below sea level, so when a levee is breached, Bay water enters and is exchanged during tidal cycles. The tidal flows provide nutrients, sediments, and a means for aquatic life to repopulate these altered systems. The flooding risk is illustrated in the figure below taken from Mount and Lowe [2014].

This figure is a cross section through a diked wetland showing a levee at the bayshore side that would be removed and the need for an inland levee to protect against high water and wind generated waves. The presence of vegetated, shallow water in the restored area lowers wave heights and inland levees can be lower in height than the bayshore levee. Anticipating sea level rise would require additional height of the inland levee.

The figure does simplify the flooding hazard of beached levees. In the case of salt ponds that ring the South Bay, there exists a bayshore levee as well as an inland levee to protect residential (Alviso), commercial (Google), transportation corridors (Highway 237) and critical governmental facilities (wastewater treatment) from flooding risks. If the bayshore levees are removed during a restoration effort, then any existing inland levees separating the wetland from the developed land will be inadequate protection for the 100-year flood at current and future sea level conditions. The Authority has prepared a map of sites that would qualify for restoration funding. That map also includes an Anticipated Levee Project that shows an extensive network of inland levees that are mostly in the South Bay, south of the San Mateo Bridge []. As a consequence, wetlands restoration of the salt ponds in the South Bay will require extensive levee construction at the inland interface, and the magnitude of flood mitigation efforts is not separately addressed in the Authority’s analysis of possible projects.

Policy, Planning, and Monitoring

The three recent reports summarized in the Background section to follow are consistent in their assessment of problems with environmental restoration policies, how permits are issued as part of the planning process, and what effective monitoring entails to demonstrate achievement of project goals. Wetlands restoration is a new science and the tools are not fully developed that allow projects to be designed and implemented with certain outcomes. Even the term “restoration” is a misnomer since the San Francisco Bay and Delta have been so altered, there is no expectation that the system can be restored to its former state. The regulatory environment is cumbersome with multiple agencies having different mandates, resulting in their own permit requirements, and delays related to inadequate staffing. What is monitored is not consistent among agencies, the time period required for monitoring does not reflect the long duration necessary for the reestablishment of physical processes, the time required for the appearance of suitable habitat, and then the biological response to that habitat. An additional theme is the lack of a common approach to monitoring the evolution of the restored systems and even the sharing of the monitoring data in a timely fashion among governmental institutions.

The San Francisco Bay Restoration Authority has provided a list of approximately 90 local examples of projects anticipated to be eligible for Restoration Authority grants. These projects range from smallscale shoreline park expansions to vast salt pond restoration. The Authority will seek local funding for some of these projects, but there is no recognition of the uncertainty in achieving restoration goals and no appreciation of the need for a more efficient regulatory process.


The State of California through legislation forming the San Francisco Bay Restoration Authority has given the Bay Area an opportunity to undertake local action for restoring the unique environment of San Francisco Bay. The designated San Francisco Bay Restoration Authority was formed in 2008 and has a $12 parcel on the June 2016 general election ballot that if successful will generate $500 million over the period 2017 to 2037. It is likely that a considerable amount of that funding will be diverted to the expense associated with flood mitigation following bayshore levee breaching. The inefficiency and expense associated with managing the interactions between regulatory agencies with conflicting mandates and stakeholders has not been addressed. Former Contra Costa County Supervisor Sunne McPeak said in the early 1980s “policy before plumbing” when referring to the Delta’s then-proposed Peripheral Canal. The Authority might be held to a similar standard of “reform before restoration.”


Activities by the San Francisco Bay Restoration Authority cannot be separated from many other governmental and regulatory organizations that have been involved in efforts to improve the Bay. The year 2015 was a banner year for reports from these organizations that provide context for what wetlands restoration involves, the uncertainties, the hindrances, and the eventual costs.

Goals Project [2015]

This report by local scientists provided an update to a 1999 report that is best known for its recommendation that 100,000 acres of tidal marsh be restored in San Francisco Bay. The restoration goal was to recover half of the original tidal wetlands that were present prior to 1850 [Goals Project, 1999] The 2015 update did not change the recommended area for restoration but provided a progress report on ongoing restoration activities and new challenges associated with sea level rise. Tidal wetlands were lost to numerous activities such as filling along the shoreline, but their focus has been on salt ponds, duck club ponds, and diked agricultural land. Salt ponds ringed the South Bay while duck ponds and diked agricultural land were developed in the North Bay. The surface of the ponds and the agricultural land are below sea level, which required levees to keep the seawater out. Restoration has involved breaching these levees and allowing tidal exchange to circulate water, sediments, and nutrients leading ultimately to restoration of ecological functions in these highly altered systems.

Since 1999 a number of wetlands restoration projects were initiated and the complexity of these projects is recognized in the 2015 updates. While it is relatively easy to breach a levee to restore tidal exchange with the Bay, the regulatory processes and the monitoring of the recovery remain challenges. The federal and local agencies identified as potentially having a role in the permitting process of Bay Area wetlands projects include the US Army Corps of Engineers, the National Marine Fisheries Service, the US Fish and Wildlife Service, the US Environmental Protection Agency, the San Francisco Bay Regional Water Quality Control Board, the California Department of Fish and Wildlife, and the San Francisco Bay Conservation and Development Commission. Given the regulatory burden imposed by permit requirements, some projects have been constrained by the excessive time required to obtain the necessary permits. Given the uncertainty of the science and management of restoration, experimentation and monitoring are required. The need for experimentation and adaptation is necessary, but not always feasible in smaller projects. The updated Goals Project also identified the critical need for collecting and sharing monitoring data among regulatory agencies. However the multiple objectives of flood control, shoreline protection, and habitat enhancement could take years to achieve in a system subjected to natural cycles of droughts, floods, wind storms, and ecological succession. The anticipated acceleration in sea level rise is an additional uncertainty in project design, performance, and monitoring.

The State of the Estuary [2015]

The San Francisco Estuary Partnership is a coalition of resource agencies, non-profits, citizens, and scientists working to protect, restore, and enhance water quality and fish and wildlife habitat in and around the San Francisco Bay Delta Estuary. Besides the Bay, the partnership includes the Delta formed by the Sacramento and San Joaquin Rivers. This report provides an overview of the physical processes that form the estuary in terms of freshwater flows and sediment contribution, the status of physical habitats around the estuary, and the ecological processes that currently are operating. Environmental health for the estuary is defined based on 33 separate indicators rather than a composite. The indicators include water flows and quality, physical habitats and biological factors. The analysis is based on separate geographical regions within the estuary (South, Central, North Bays, Suisun Marsh, and the Delta). Trends over time are noted with improvements in water quality and declines in freshwater inflows. The breadth of coverage is indicated by consideration of the state of the physical and ecological system, but also human activities that contribute to health indicators such as freshwater conservation and implementation of wastewater reuse in urban areas. The report notes the long-term improvements in water quality was a direct result of investments in sewage treatment facilities around the Bay over the last 50 years. However, estuary health is compromised by legacy toxics present in the sediments and by ecosystem processes altered by flows, habitat loss, and the continuing invasion of non-native species The report does not address restoration priorities given that topic is the subject of other reports.

Comprehensive Conservation and Management Plan [2015]

This draft report was released by the San Francisco Estuary Partnership and provides an update to the Partnership’s mandate to protect and restore the estuary. The report includes 38 action items that range from protecting, restoring and enhancing various habitats within the estuary to identifying revenue sources for implementing these actions. One of the action items is to establish a regional wetland monitoring and assessment program since none currently exist, and this lack of a systematic evaluation of wetland habitats precludes learning from ongoing projects throughout the estuary. The greater number of projects that have multiple benefits has led to difficulties in coordination of regulatory agencies. For example a sediment management project can potentially improve wetlands habitat, mitigate flood risks, and improve navigation, but requires more efficient coordination among regulatory agencies. The final report in 2016 is supposed to include a chapter on monitoring and assessment but that chapter was not available in the draft document. As with other reports on the San Francisco Estuary, anticipating the consequences of sea level rise has become a far greater challenge than identified in previous reports.


Comprehensive Conservation and Management Plan [2015] San Francisco Estuary Partnership, Draft, September 17, 2015,
Goals Project [1999] Baylands Ecosystem Habitat Goals. A report of habitat recommendations prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project. U.S. Environmental Protection Agency, San Francisco, Calif./S.F. Bay Regional Water Quality Control Board, Oakland, Calif. .
Goals Project [2015] The Baylands and Climate Change: What We Can Do. Baylands Ecosystem Habitat Goals Science Update 2015 prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project. California State Coastal Conservancy, Oakland, CA.
J. Mount and J. Lowe [2014] Flooding in San Francisco Bay: Risks and Opportunities, Resources Legacy Fund, Sacramento, CA, January 2014,
Save the Bay [2007] Greening the Bay, Financing Wetland Restoration in San Francisco Bay,
Save the Bay [2011] Political Feasibility Analysis for SF Bay Restoration Authority, October 26, 2011, Presented by Storefront Political Media.
The State of the Estuary [2015] San Francisco Estuary Partnership,