Skip to main content
Open Access Publications from the University of California


SFEWS provides credible scientific information on California's complex water issues, linking new science to policy with great effect. SFEWS retains a regional focus on the San Francisco Bay and the Sacramento–San Joaquin Delta, also known as the Bay–Delta watershed. At the heart of open access from the California Digital Library, SFEWS's scholarly output ranks #1 for the UC Davis Institute  of the Environment and ranks #3 campus wide.

Volume 1, Issue 1, 2003

Research Article

An Introduction to the San Francisco Estuary Tidal Wetlands Restoration Series

Restoration of tidal wetlands may provide an important tool for improving ecological health and water management for beneficial uses of the San Francisco Estuary (hereafter “Estuary”). Given the large losses of tidal wetlands from San Francisco Bay and the Sacramento-San Joaquin Delta in the last 150 years, it seems logical to assume that restoring tidal wetlands will have benefits for a variety of aquatic and terrestrial native species that have declined during the same time period. However, many other changes have also occurred in the Estuary concurrent with the declines of native species. Other factors that might be important in species declines include the effects of construction of upstream dams, large and small water diversions within the Sacramento-San Joaquin Delta, agricultural pesticides, trace elements from industrial and agricultural activities, and invasions of alien species. Discussions among researchers, managers, and stakeholders have identified a number of uncertainties regarding the potential benefits of tidal wetland restoration. The articles of the Tidal Wetlands Restoration Series address four major issues of concern. Stated as questions, these are:

1. Will tidal wetland restoration enhance populations of native fishes?

2. Will wetland restoration increase rates of methylation of mercury?

3. Will primary production and other ecological processes in restored tidal wetlands result in net export of organic carbon to adjacent habitats, resulting in enhancement of the food web? Will the carbon produced contribute to the formation of disinfection byproducts when disinfected for use as drinking water?

4. Will restored tidal wetlands provide long-term ecosystem benefits that can be sustained in response to ongoing physical processes, including sedimentation and hydrodynamics?

Reducing the uncertainty surrounding these issues is of critical importance because tidal wetland restoration is assumed to be a critical tool for enhancement of native species and ecosystem processes in the Estuary.

Will Tidal Wetland Restoration Enhance Populations of Native Fishes?

Restoration of tidal wetlands might enhance populations of native fishes in the San Francisco Estuary of California. The purpose of this paper is to: (1) review the currently available information regarding the importance of tidal wetlands to native fishes in the San Francisco Estuary, (2) construct conceptual models on the basis of available information, (3) identify key areas of scientific uncertainty, and (4) identify methods to improve conceptual models and reduce uncertainty. There are few quantitative data to suggest that restoration of tidal wetlands will substantially increase populations of native fishes. On a qualitative basis, there is some support for the idea that tidal wetland restoration will increase populations of some native fishes; however, the species deriving the most benefit from restoration might not be of great management concern at present. Invasion of the San Francisco Estuary by alien plants and animals appears to be a major factor in obscuring the expected link between tidal wetlands and native fishes. Large-scale adaptive management experiments (>100 hectares) appear to be the best available option for determining whether tidal wetlands will provide significant benefit to native fishes. Even if these experiments are unsuccessful at increasing native fish populations, the restored wetlands should benefit native birds, plants, and other organisms.

Potential Effects of Organic Carbon Production on Ecosystems and Drinking Water Quality

Restoration of tidal wetlands in the Sacramento-San Joaquin Delta (Delta) is an important component of the Ecosystem Restoration Program of the CALFED Bay-Delta Program (CALFED). CALFED is a collaborative effort among state and federal agencies to restore the ecological health and improve water management of the Delta and San Francisco Bay (Bay). Tidal wetland restoration is intended to provide valuable habitat for organisms and to improve ecosystem productivity through export of various forms of organic carbon, including both algae and plant detritus. However, the Delta also provides all or part of the drinking water for over 22 million Californians. In this context, increasing sources of organic carbon may be a problem because of the potential increase in the production of trihalomethanes and other disinfection by-products created during the process of water disinfection. This paper reviews the existing information about the roles of organic carbon in ecosystem function and drinking water quality in the Bay-Delta system, evaluates the potential for interaction, and considers major uncertainties and potential actions to reduce uncertainty. In the last 10 years, substantial progress has been made on the role of various forms of organic carbon in both ecosystem function and drinking water quality; however, interactions between the two have not been directly addressed. Several ongoing studies are beginning to address these interactions, and the results from these studies should reduce uncertainty and provide focus for further research.

Potential for Increased Mercury Accumulation in the Estuary Food Web

Present concentrations of mercury in large portions of San Francisco Bay (Bay), the Sacramento-San Joaquin Delta (Delta), and the Sacramento and San Joaquin rivers are high enough to warrant concern for the health of humans and wildlife. Large scale tidal wetland restoration is currently under consideration as a means of increasing populations of fish species of concern. Tidal wetland restoration activities may lead to increased concentrations of mercury in the estuarine food web and exacerbate the existing mercury problem. This paper evaluates our present ability to predict the local and regional effects of restoration actions on mercury accumulation in aquatic food webs. A sport fish consumption advisory is in place for the Bay, and an advisory is under consideration for the Delta and lower Sacramento and San Joaquin rivers. Mercury concentrations in eggs of several water bird species from the Bay have exceeded the lowest observed effect level. A variety of mercury sources, largely related to historic mercury and gold mining, is present in the watershed and has created a spatially heterogeneous distribution of mercury in the Bay-Delta Estuary. Mercury exists in the environment in a variety of forms and has a complex biogeochemical cycle. The most hazardous form, methylmercury, is produced at a relatively high rate in wetlands and newly flooded aquatic habitats. It is likely that distinct spatial variation on multiple spatial scales exists in net methylmercury production in Bay-Delta tidal wetlands, including variation within each tidal wetland, among tidal wetlands in the same region, and among tidal wetlands in different regions. Understanding this spatial variation and its underlying causes will allow environmental managers to minimize the negative effects of mercury bioaccumulation as a result of restoration activities. Actions needed to reduce the uncertainty associated with this issue include a long term, multifaceted research effort, long term monitoring on local and regional scales, and careful evaluation of individual restoration projects with regard to potential increase of food web mercury.

Will Restored Tidal Marshes Be Sustainable?

We assess whether or not restored marshes in the San Francisco Estuary are expected to be sustainable in light of future landscape scale geomorphic processes given typical restored marsh conditions. Our assessment is based on a review of the literature, appraisal of monitoring data for restored marshes, and application of vertical accretion modeling of organic and inorganic sedimentation. Vertical accretion modeling suggests that salt marshes in San Pablo Bay will be sustainable for moderate relative sea level rise (3 to 5 mm yr-1) and average sediment supply (c. 100 mg L-1). Accelerated relative sea level rise (above 6 mm yr-1) and/or reduced sediment supply (50 mg L-1) will cause lowering of the marsh surface relative to the tide range and may cause shifts from high to low marsh vegetation by the year 2100. Widespread conversion of marsh to mudflat-"ecological drowning"-is not expected within this time frame. Marshes restored at lower elevations necessary to aid the natural development of channel systems (c. 0.5 m below mean higher high water) are predicted to accrete to high marsh elevations by the year 2100 for moderate relative sea level rise and sediment supply conditions. Existing rates of sediment accretion in restored fresh water tidal marshes of the Delta of greater than 9 mm yr-1 and slightly lower drowning elevations suggest that these marshes will be resilient against relatively high rates of sea level rise. Because of higher rates of organic production, fresh water marshes are expected to be less sensitive to reduced sediment availability than salt marshes. The ultimate long-term threat to the sustainability of tidal marshes is the interruption of coastal rollover-the process by which landward marsh expansion in response to sea level rise compensates for shoreline erosion. Bay front development now prevents most landward marsh expansion, while shoreline erosion is expected to accelerate as sea level rises.

A Summary of the San Francisco Tidal Wetlands Restoration Series

The four topical articles of the Tidal Wetlands Restoration Series summarized and synthesized much of what is known about tidal wetlands and tidal wetland restoration in the San Francisco Estuary (hereafter “Estuary”). Despite a substantial amount of available information, major uncertainties remain. A major uncertainty with regard to fishes is the net benefit of restored tidal wetlands relative to other habitats for native fishes in different regions of the Estuary given the presence of numerous invasive alien species. With regard to organic carbon, a major uncertainty is the net benefit of land use change given uncertainty about the quantity and quality of different forms of organic carbon resulting from different land uses. A major challenge is determining the flux of organic carbon from open systems like tidal wetlands. Converting present land uses to tidal wetlands will almost certainly result in increased methylation of mercury at the local scale with associated accumulation of mercury within local food webs. However, it is unclear if such local accumulation is of concern for fish, wildlife or humans at the local scale or if cumulative effects at the regional scale will emerge. Based on available information it is expected that restored tidal wetlands will remain stable once constructed; however, there is uncertainty associated with the available data regarding the balance of sediment accretion, sea-level rise, and sediment erosion. There is also uncertainty regarding the cumulative effect of many tidal restoration projects on sediment supply. The conclusions of the articles highlight the need to adopt a regional and multidisciplinary approach to tidal wetland restoration in the Estuary. The Science Program of the CALFED effort provides an appropriate venue for addressing these issues.