Our Programs

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The Regional Monitoring Program (RMP) is SFEI’s largest program and monitors contamination in the Estuary. It provides water quality regulators with information they need to manage the Estuary effectively. The RMP is an innovative collaborative effort between SFEI, the Regional Water Quality Control Board, and the regulated discharger community. Read More...
SFEI is the science lead for the San Francisco Bay Nutrient Science and Management Strategy, which is developing the science needed for informed decisions about managing nutrient loads and maintaining beneficial uses within the Bay. Two recent products highlight key initiatives of this Program. Read More...
The SF Chronicle features a story describing how scientists have found evidence of widespread and rapid declines in flame retardant pollution in many San Francisco Bay species, according to a new study released by the San Francisco Estuary Institute. Read More...

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California's EcoAtlas provides access to information for effective wetland management. The maps and tools can be used to create a complete picture of aquatic resources in the landscape by integrating stream and wetland maps, restoration information, and monitoring results with land use, transportation, and other information important to the state’s wetlands. Read More...
The Riparian Zone Estimator Tool (RipZET) is a GIS-based decision-support tool under development for estimating riparian zones at the watershed and/or project scale. The tool provides reach-scale functional riparian width estimates based on average height of mature riparian vegetation, the steepness of hillslopes adjacent to the channel, and the floodplain inundation extent for large storm events. The appropriate width estimate for a reach is then determined based on the riparian functions associated with different channel types, which range from steep headwater channels to low-gradient, meandering channels with broad floodplains. Read More...
Contaminant Data Display and Download Tool or CD3 is an innovative visualization tool that enables users to perform spatial queries for water quality data from the San Francisco Estuary and Delta. Data can be dynamically mapped and downloaded as an Excel file. New datasets are regularly made available through this tool. Read More...

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A Delta Transformed: Ecological Functions, Spatial Metrics, and Landscape Change in the Sacramento-San Joaquin Delta provides the first analysis of landscape ecology metrics in the pre-disturbance and contemporary Delta to help define, design, and evaluate functional, resilient landscapes for the future. Read More...
The Northern San Diego County Lagoons Historical Ecology Investigation draws on hundreds of historical documents to analyze and reconstruct historical landscape conditions for six northern San Diego County estuaries prior to the major modifications of the late 19th and 20th centuries. This study shows that the lagoons experienced highly dynamic, variable environmental conditions and supported a diverse array of habitats and native species in the recent past. Though the lagoons have experienced widespread transformation over the past centuries, elements of the lagoon ecosystems have persisted. Read More...
Flood Control 2.0 is an ambitious regional effort aimed at helping restore stream and wetland habitats, water quality, and shoreline resilience around San Francisco Bay. The project leverages local resources from several forward-looking flood control agencies to redesign major flood control channels so that they provide both future flood conveyance and ecological benefit under a changing climate. Read More...