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Program Information

Overview | Objectives | History | Recent Findings

Program Overview:

Large amounts of public funds and human resources are being invested in the protection, creation, restoration, and enhancement of wetlands in the Region. Both the number and size of wetland projects are increasing each year, and the overall ecological and economic importance of wetlands is therefore also increasing.

A monitoring program is needed to evaluate wetland policies, programs, and projects in the Region. Wetlands need to be compared to one another and over time, relative to ambient conditions, to assess the status and trends of the wetland ecosystem, measure the progress of wetland projects, measure the effects of the projects on the larger ecosystem, troubleshoot problems, assess the efficacy of management decisions, and otherwise account for the public investment in wetlands.

But these needs cannot be met at this time because the ambient conditions of wetlands are not being monitored, projects are monitored in disparate ways, there is little assurance of data quality, and monitoring results are not readily available.

Through this program, SFEI helps the regional client community of wetland interests to reach consensus about the highest priority needs for scientific information about wetlands, to define SFEI’s roles in meeting those information needs, and SFEI plays the roles to the satisfaction of the community.

Program Objectives:

Coordinate the design and implementation of a regional program to monitor the status and trends of the wetland ecosystem of the San Francisco Estuary.

  • Contribute to the scientific basis for wetland conservation, to the assessment of the success (or failure) of wetland restoration projects, and to the assessment of the ecological effects of wetland management including restoration.
  • Create and maintain a regional public access information system about wetlands in the region.
  • Enhance coordination of wetland research within the region between and among state and federal agencies and academia.
  • Enhance coordination of monitoring and research that regards wetlands as transitional landscapes between terrestrial and aquatic systems.


Program History:

Between 1995 and 1999, the priority need was to help determine how much of what kinds of wetlands are needed where, and why. SFEI played a central role in defining the question, advancing the process of getting answers, and reporting the answers to the public. The primary products were the Bay Area Wetlands Ecosystem Habitat Goals Report and the Baylands Ecosystem Species and Community Profiles. More important has been the surge in ecological restoration and the invigorated culture of scientific collaboration and integration that have been nurtured by the Goals Project.

Since 1999, the highest priority need has shifted from getting consensus about restoration goals to tracking the progress of restoration projects, and assessing their ecosystem effects. To meet this need, SFEI has been coordinating scientific efforts among many agencies and science institutes to design and implement a Wetland Regional Monitoring Program (WRMP). The effort is intensive, iterative, open-ended, and productive. It continues to yield significant original data and findings on many major aspects of the wetlands ecosystem. The WRMP is poised to be adopted by the new multi-agency SF Bay Wetland Recovery Program as its monitoring element.

The Wetland Science Program has given rise to three important regional science initiatives that are centered at SFEI. The EcoAtlas Information System, the Historical Ecology Project, and the Watershed Program are growing ventures of regional scientific importance and celebrity that have grown from the Wetlands Science Program.

Wetlands have always been viewed as transitional landscapes between aquatic and terrestrial environments. The Wetlands Science Program has been strategically planned for collaboration with aquatic and terrestrial programs and projects, including especially SFEI’s Regional Monitoring Program for Trace Substances and Watersheds Program.


Selected Findings:

In 1995, we produced the first Regional Wetlands Monitoring Plan for the San Francisco Bay Area. This was a landmark document that summarized existing conceptual models of wetland form and function, outlined a system of wetland classification, a process to establish regional wetland habitat goals, a process to monitor wetland project performance relative to ambient conditions, and an outline for multi-agency and multi-discipline governance of the program. Most of these recommendations have since been implemented or are being implemented at this time. The most significant finding of this plan was that successful conservation of wetland resources depended upon quantitative habitat goals shared by all the wetland agencies.

  • Between 1995 and 1998, the Wetland Science Program produced the first comprehensive map of historical habitats for the region. This initiated the Historical Ecology Project and gave rise to similar efforts in other regions. The historical array of wetlands and riparian habitats was much different than had been assumed by the regional community of environmental scientists and managers. Our findings that most local streams did not naturally reach the Bay, that many of their tributaries did not reach the valley bottoms, that riparian zones were narrow and discontinuous, that complexes of vernal pools and wet coastal meadows with large stands of willows dominated the large valleys and bay-upland ecotone, that runoff from local watersheds created ecologically significant estuarine gradients, and that tidal marshes provided much of the foraging and resting habitats of migratory waterfowl have caused major paradigm shifts in the expectations for ecological restoration.
  • Our continuing study of historical wetlands and related habitats is finding that the historical habitat array that figures prominently in restoration goals was not natural but rather the result of ongoing land management by indigenous peoples. This has major implications for how people might be involved in the management of restoration projects in the future.
  • In 1996, the Wetland Science Program produced the first assessment of the potential impacts of large-scale tidal marsh restoration on existing ecological resources of the bayshore. Though controversial at the time, our main finding that significant negative impacts could be mitigated by matching restoration endpoints to specific site conditions, using dredged sediment to nurture evolution of intertidal habitats, recognizing the different ecological services of successional seres, using projects as opportunities to test different restoration techniques, and expanding the schedule of restoration to prevent over-taxing the sediment supply are now key aspects for restoration planning.
  • Also in 1996, the Wetland Science Program produced the first regional Geographic Information System (GIS) for estuarine wetlands and related habitats. The GIS, named the Bay Area EcoAtlas, enabled us to quantitatively compare past and present wetland habitat arrays. It was also used to create the first GIS-based ecological and economic cost-benefit analysis for large-scale conversion of diked baylands to tidal marsh, which showed that initial tidal elevations of re-use sites and their distance from offloading facilities controlled the economic feasibility. The finding was used by the LTMS in its initial feasibility analyses.
  • In 1997 and 1998, we found that the habitat boundaries as shown in the EcoAtlas were more precise, more accurate, and better documented that for any other map of historical habitats in the region. In part because of this finding, the Bay Conservation and Development Commission, the County of Marin, and the State Lands Commission adopted the historical baylands map for baylands planning and management.
  • In 1999 we produced the baylands Ecosystem Goals Report that has become the foundation for restoration projects large and small throughout the region. Many of the recommendations made in the original 1995 Regional Wetlands Monitoring Plan are repeated in this “Goal Report.” The process of setting the Goals was invented by us and we coordinated the scientific support. As we predicted and intended, the Goals Report is the single most important unifying element in the regional effort to restore the wetland ecosystem.
  • Also in 1999, we produced a detailed map of the historical and existing geographic extent of freshwater influences on the ecology of the intertidal zone and shallow subtidal habitats of the South Bay. The major findings that current non-saline discharges from POTWs and local creeks about match the historical discharges from local creek and springs, and that these kinds of discharges historically produced natural estuarine gradients in Far south Bay has caused the wetland agencies to begin considering the potential beneficial uses of the existing discharge as part of the large scale South Bay restoration program.
  • In 1999 and 2000, we participated in field and laboratory studies of the paleo-ecological nature of tidal marshes along the main estuarine gradient of San Francisco Bay. Our published finding that saline conditions have waxed and waned as far upstream as the western Delta since at least 2,500 years before the present challenges the general assumptions that Holocene estuarine transgression has been uniform and that the saline conditions induced by land use and water management since the mid a800s lack precedent in this system.
  • In 2000 and 2001, we sponsored and participated in studies of tidal marsh food webs in this region that suggest separate pathways of energy processing for the tidal marsh plain (which is linked to terrestrial food webs), large channels (which are linked to food webs of the tidal flats and open bays), and small intertidal channels (these seem to support their own food webs with weak links to the marsh plain and large channels). These findings are likely to strongly affect future research and monitoring for wetland project performance and intertidal contamination.
  • In 1999 and again in 2001, we planned and participated in a regional survey of the distribution and abundance of invasive cordgrass (Spartina spp.) in San Francisco Bay. The latest survey stands as the best regional picture of the non-native cordgrass invasion. Our findings of multiple invasion fronts, many forms of the invader, complex variations in percent cover within patches of the invader, abundant invasion of the tidal reaches of local creeks, and the extension of the invasion from South Bay to Central Bay has significantly shaped the emerging plan for non-native cordgrass control.
  • In 2002, we conducted the only definitive field study of the vertical distribution of non-native Spartina alterniflora and its hybrids along the South Bay shoreline and adjacent creeks. We found that the vertical distribution is less than had been assumed by the wetland management agencies. We also found a strong correlation between the minimum tidal distribution and the cumulative duration of tidal inundation during the growing season that provides a basis to predict the likely maximum extent of tidal flat conversion to cordgrass marshland under saline conditions. These findings should significantly improve the scientific basis of efforts to control the cordgrass invasion