SFEI generates reliable, sound data to drive reliable science and thoughtful decision-making. We strive to make our data and tools easy to use and accessible to everyone. In addition, since 2007, SFEI has served as one of three Regional Data Centers (RDC) that contribute water quality data to the California Environmental Data Exchange Network (CEDEN), specifically for the San Francisco Bay-Delta and northern montane regions.
The datasets listed below comprise only a subset of the extensive data we offer at SFEI. Additional datasets can be found on EcoAtlas, related to wetlands and associated restoration project tracking across the state, and the Contaminant Data Display and Download Tool (CD3), related to contaminants around San Francisco Bay and beyond.
We also refer you to a number of decision support tools that might assist with your landscape scenario and green stormwater infrastructure planning. Perhaps you are concerned about harmful algal blooms or groundwater rise. We encourage you to explore the many features below.
In any case, if you have difficulty finding the data you are looking for, please contact us at [email protected].
The California Aquatic Resources Inventory (CARI) is a Geographic Information System (GIS) dataset of wetlands, streams, and riparian areas consisting of polygon and line features that are standardized to a common wetland classification system. This statewide dataset is hosted online through EcoAtlas to support the state’s Wetland and Riparian Area Protection Policy (WRAPP).
The Baylands Habitat Map 2020 (BHM2020) represents the condition of the San Francisco Bay Baylands in the year 2020. It was first published in April 2024. It was developed to meet the needs of the San Francisco Estuary Wetlands Regional Monitoring Program's (WRMP) by mapping habitat types for the purpose of monitoring regional change over time using primarily remote sensing data.
These are the official segments and associated boundaries for the Regional Monitoring Program (RMP) for Water Quality in San Francisco Bay. This geodatabase contains four layers:
The Santa Clara Valley Water District (Valley Water) is a California Special District water resources agency in Santa Clara County providing safe, clean water for a healthy life, environment and economy, flood protection, and stewardship of streams on behalf of the county’s residents. Over the last two decades the Santa Clara County voters approved the Safe, Clean Water and Natural Flood Protection Program that identified a number of local priorities.
The TPW mobile app is a tool designed to make tobacco and nicotine trash data collection easier, more consistent across TPW campaigns, geographic differences, while conducted in a scientifically valid way. The app is based on the survey methods and protocol in the California Trash Monitoring Methods and Assessments Playbook, which was developed by San Francisco Estuary Institute (SFEI) to ensure comparable information across different geographies, time, and practitioners.
This mapping depicts the historical habitat types and channels of the Morro Bay estuary, the sandspit, and alluvial portions of Chorro Valley, Los Osos Valley, and lower Morro Creek downstream of highway 1, representing prevailing ecological conditions prior to substantial Euro-American modification (mid-1800s). The study area encompasses approximately 59 km2 (23 mi2) of the Morro Bay Watershed, but excludes the surrounding hillslopes outside of the valley floor areas. This project was funded by a grant from the U.S.
The Russian River Aquatic Resource Inventory (RRARI) is an inventory of aquatic resources and their associated vegetated areas in the Russian River Watershed and Sonoma County in California. The inventory was largely developed using an automated approach consisting of a computer algorithm developed by GIS staff, to apply a standardized and regionally relevant classification system in order to support environmental planning and resource management tracking at a local and regional scale.
This dataset provides building-level estimates of population and selected demographic characteristics, for the nine Bay Area counties (Alameda, Contra Costa, Marin, Napa, San Francisco, San Mateo, Santa Clara, Solano, and Sonoma), by redistributing American Community Survey (ACS) data (2017-2021) from census block groups to individual residential buildings. The purpose of this dataset is to support planning, analysis, and decision-making efforts that require a more spatially realistic representation of where people live than is available from census geographies alone.
The Moored Sensor Program (MSP) is a network of high-frequency continuous water quality sensors distributed throughout San Francisco Bay. The network was first established in 2013 as part of the Nutrient Management Strategy, a program tasked with building the scientific foundation needed to inform nutrient-related management decisions in the Bay. The MSP has grown from two monitoring sites to more than fourteen, with more anticipated.
These data layers accompany the 2025 Petaluma River Watershed Sediment Source Assessment, part of the San Francisco Estuary Institute’s (SFEI) larger Sediment Solutions project funded by the U.S. EPA and Sonoma Water. Information on the project can be found at www.sfei.org/sedimentsolutions. These datasets are intended to allow for use of the mapped sediment supply data displayed in the sediment source assessment report, as well as define boundary areas for subcatchments assessed in the project.
This data package is a key deliverable for the Research to Understand Impacts of Bay Sand Mining on Sand Supply and Transport in San Francisco Bay and the Outer Coast project.
The following existing data sources were compiled at the beginning of this project:
1. Bay Segments
2. 2018 Bathy Survey Data
This data package is a key deliverable for the Research to Understand Impacts of Bay Sand Mining on Sand Supply and Transport in San Francisco Bay and the Outer Coast project.
This data package is a key deliverable for the Research to Understand Impacts of Bay Sand Mining on Sand Supply and Transport in San Francisco Bay and the Outer Coast project.
This data package is a key deliverable for the Research to Understand Impacts of Bay Sand Mining on Sand Supply and Transport in San Francisco Bay and the Outer Coast project.
This is a geospatial dataset (feature class within a file geodatabase) of output from the Riparian Zone Estimation tool (RipZET). RipZET estimates functional riparian extent around stream and wetland features based on modelled vegetation and hillslope processes. This dataset includes the Russian River Watershed, Sonoma County, and a small northern portion of Marin County. It was derived from Caltrans_CARIv2.0 which is a polygon only version of CARI.
This preliminary coarse-scale mapping depicts the historical habitat types and channels of the core river-wetland corridor of the Sacramento Valley, representing average conditions prior to substantial Euro-American modification (mid-1800s). They include the Sacramento River, adjacent riparian forest and major wetland areas within the valley’s flood basins. This covers the American, Sutter, Colusa and Butte basins; the Sacramento and Yolo basins were included in the Sacramento-San Joaquin Delta Historical Ecology Investigation (Whipple et al. 2012).
The metrics describe elements of baylands resilience associated with wildlife support, flood attenuation, and the feasibility of sediment placement. These metrics are the first tranche to be mapped; future efforts will map additional metrics associated with wildlife support and flood attenuation, and create metrics for additional ecosystem services like carbon sequestration and water quality improvement.
The Project Tracker Tidal Wetland Restoration Map (Restoration Map) dataset provides spatial boundaries and key attributes of restored tidal wetlands in the San Francisco Bay.
This page provides access to tabular data (in excel format) summarized in a Russian River Regional Monitoring Program’s (R3MP) report completed in 2025.
This geodatabase contains historical habitat channel mapping representing prevailing channel configuration in Suisun Marsh and surrounding upland areas in the early 1800s, prior to major Euro-American modification.
This is a modification of the MTC 2020 Land Use layer provided to SFEI by MTC. SFEI has collaborated with MTC to add additional fields that provide important information for water quality scientists and modelers. The first comprehensive information on Bay Area land use was released by ABAG in 1995, updated in 2000, and again in 2005 to reflect the (then) latest information about land use on a parcel basis. The 2005 dataset has since been used for a wide range of applications (both inside and outside of ABAG), most of which it was never designed to support.
The WRMP Subembayments were created from grouping Operational Landscape Units (OLUs) into divisions of the San Francisco Bay/ Lower San Francisco Estuary that were similar from a natural process and ecological standpoint. This Subembayments layer is intended to be used for reporting and planning purposes for the WRMP.
Since the 1990s, a variety of partnerships including federal, state, local agencies, and non-governmental organizations have been developing maps and other information about the distribution, abundance, and diversity of aquatic, wetland, and terrestrial habitat types at the time of European contact in various regions of California. Most of the efforts summarized here follow a methodology of historical ecology research developed by the San Francisco Estuary Institute (SFEI).
San Diego Aquatic Resource Inventory (SDARI) is a detailed base map of the San Diego Regional Water Board aquatic features. SDARI was developed using a Geographic Information System (GIS) and semi-automated object based image analysis (OBIA) leveraging both machine learning and rule based classification models. The mapping models use high resolution four band imagery, LiDAR, and a suite of ancillary data sources to consistently map aquatic resources throughout the San Diego region of interest.
This study focuses on a segment of the Santa Ana River Parkway in and around the City of Riverside, where multiple habitat restoration projects are underway.
This work was completed in 2023 and funded by the California Department of Transportation. Individual vernal pools were mapped within the Carol Witham complex polygons where high resolution lidar data was available, approximately 83% of the complex polygon area. SFEI attempted to map the remaining complex polygons without lidar data, however without lidar and high resolution time series data the results were not compelling enough to include in this final dataset. Data used to map pools included 3DEP high resolution lidar sourced from the years 2007 - 2022, NAIP 2018, and NAIP 2020.
This dataset includes depth-to-groundwater maps produced by Pathways Climate Institute and San Francisco Estuary Institute with funding from the Bay Area Council's California Resilience Challenge and the Regional Water Quality Control Board. For more information, please visit the project page.
Each link below is a zipped file containing a geodatabase (GDB). There is one zip file for each county covered by this analysis. Each zipped GDB contains:
Despite California's data-rich environment, there are still many obstacles when trying to access and understand pesticide data at the nexus of water quality, ecological effects, and human health. We recognize a need to fill data gaps, not necessarily by collecting new data, but by better leveraging information already technically in the public domain. The goal of this project is to bring pesticide reporting, occurrence, and toxicity data together in ways that yield insights and meet the expressed needs of stakeholders in clear, efficient, credible, and repeatable ways.
This page provides public access to tabular datasets for the CRAM Habitat Development Curves (HDCs) and statewide and regional probablity based ambient survey Cumulative Distribution Function estimate curves (CDFs) found in EcoAtlas.
This mapping documents the changes in extent and condition of vernal pool habitat in the Great Valley between 2005 and 2018. It also inlcudes information based on a 2012 remapping effort. "Vernal pool habitat" is defined as vernal pools and the surrounding upland (typically grassland) habitat matrix. The result of the 2018 remapping shows 735,820 acres of extant habitat. This is down from 2005, a net reduction of 70,482 acres.
The completion of the Delta Aquatic Resource Inventory (DARI) dataset provides a basemap allowing the quantification of aquatic resources and related habitats within the Sacramento-San Joaquin River Delta (Delta). DARI maps all channels and wetlands, including woody wetlands such as wetlands vegetated with willows, and thus may partially capture riparian areas, however, it does not include polygons for riparian areas. Riparian areas are important to capture as their loss has affected water quality and habitat conditions and presented a number of challenges for resource managers related to…
Delta Aquatic Resource Inventory (DARI) is a detailed base map of the Sacramento-San Joaquin Delta's aquatic features that include wetlands, open water, streams, ditches, and tidal marshes. DARI was developed using a Geographic Information System (GIS) and heads up digitizing, with true color imagery, LiDAR, and a suite of ancillary data sources to consistently map aquatic resources throughout the Delta. The draft GIS dataset was reviewed by regional wetland scientists and stakeholders to ensure it is accurate as possible.
Designed to inform climate change adaptation planning, the Landscape Scenario Planning Tool (LSPT) helps users create land use scenarios, efficiently evaluate their benefits and tradeoffs, and quantify progress towards regional goals. Bringing together a decade of research and peer-reviewed methods, the LSPT has been used by agencies, planners, and researchers to envision a healthy and resilient Delta and Suisun Marsh.
Through an EPA-funded Wetland Development Grant, Permit Sonoma, County of Sonoma (County), in coordination with the Sonoma Ecology Center (SEC), the San Francisco Estuary Institute (SFEI), and a Technical Advisory Committee (TAC), developed the Sonoma County Riparian Corridor Mapping Pilot Study (Pilot Study). The Pilot Study is Permit Sonoma’s initial step in the development of an automated GIS method to update its riparian mapping database countywide using LiDAR derived stream data.
SFEI will leverage its experience as a Regional Data Center for CEDEN to deliver a scientifically sound data management strategy and plan for the Habematolel Pomo of Upper Lake (HPUL) and the Lake County Watershed Protection District (District). The main tasks for Phase 1 include summarizing existing and water quality data currently being collected in Lake County, developing templates and guidance for uploading data, formatting and exchanging data with the California Environmental Data Exchange Network (CEDEN) and USEPA's Water Quality Exchange (WQX), and preparing user-friendly factsheets…
This dataset includes all replication materials for Spotswood et al. 2021 ‘Nature inequity and higher COVID-19 case rates in less green neighbourhoods in the United States’. The materials allow users to reproduce analyses, figures, and calculations appearing the main text and extended data of the paper. This site hosts ArcGIS shapefiles with all relevant data and R code to reproduce all analyses and figures. See manuscript methods for further details for data preparation and sources.
This dataset is an ArcGIS map package containing the Operational Landscape Units and nature-based shoreline adaptation opportunities described in the San Francisco Bay Shoreline Adaptation Atlas. The map package includes the following layers:
The California Ocean Protection Council (OPC), in close partnership with the State Water Board, has recognized the importance of standard methods for trash monitoring and has funded this project. The Southern California Coastal Water Research Project (SCCWRP) and San Francisco Bay Estuary Institute (SFEI) have partnered up to test multiple trash monitoring methods with a goal of developing a library of methods with known levels of precision, accuracy, and cross-comparability of results, and linking these methods to specific management questions.
The Coyote Creek Native Ecosystem Enhancement Tool (CCNEET, neet.ecoatlas.org) is an online decision-support tool to identify opportunities to improve ecological conditions. CCNEET was inspired by the need for a watershed approach to environmental resource management. Available ecological and environmental information is synthesized by objectives, management questions, and enhancement actions to identify and justify potential habitat improvements along the creek corridor. The overarching goal of CCNEET is to help coordinate habitat conservation and enhancement along so that multiple…
Pathways Climate Institute and SFEI produced depth to groundwater maps to inform sea level rise adaptation efforts in Alameda, Marin, San Mateo, San Francisco, and Contra Costa Counties.
Sediment bulk density is the total mass of mineral and organic sediment within a defined volume. It is a key variable in many research questions pertaining to Bay sediment studies but one that is often poorly quantified and can be misinterpreted. The motivation for this report comes from a recommendation by Schoellhamer et al. (2018) to compile more accurate estimates of bulk density of Bay sediments to convert between volume and mass with a higher level of certainty.
An R-package for spatial and temporal analysis of floodplain inundation characteristics and application of habitat suitability criteria. It takes as input raster data of depth and velocity (e.g., from 2D hydrodynamic modeling) at known flows and a corresponding daily flow time series. Daily rasters of estimated depth and velocity are generated from inputs using spatially resolved piece-wise linear interpolation. Hydrospatial analysis functions calculate a range of physical metrics using the raster time series. Habitat suitability criteria applied to the…
In partnership with the Bay Conservation and Development Commission, SFEI's Environmental Informatics team built the Bay Shoreline Flood Explorer, a tool that allows you to visualize sea level rise and flood risk projections. Design plays an important role in the tool, from establishing a strong brand to conveying technical data using colors and symbologies that are easy to understand. These elements help improve the user experience and amplify the tool’s impact: by easily visualizing the consequences of flooding, planners and decision makers can more effectively identify and prioritize…
As a continuation of our collaboration with BCDC and the Adapting to Rising Tides (ART) team, the technical team at SFEI has developed a new version of the sea-level rise visualization tool which focuses on East Contra Costa and the Delta. The East Contra Costa Shoreline Flood Explorer incorporates regionally specific data that takes into account inundation and flooding information as a product of riverine flooding and sea-level rise. The map visualizes these data in conjunction with storm events and makes it available…
15 Separate analysis layers were developed to help identify suitable Chinook salmon rearing habitat in the Sacramento-San Joaquin Delta. Descriptions of these layers are provided below
The objective of this project is to summarize existing research and knowledge around suitable rearing habitat for Chinook salmon in the Sacramento-San Joaquin Delta; identify areas of suitability for rearing salmon using a combined suitability analysis of four mapped habitat parameters; and to provide recommendations for types of restoration needed to improve or restore rearing habitat, as well as to identify where in the Delta these restoration efforts could be prioritized.
EcoAtlas is a set of tools for visualizing, sharing, summarizing, and reporting on standardized geospatial environmental datasets of stream and wetlands extent and conditions. Tools include the Landscape Profile Tool and summary Dashboards. EcoAtlas broadly supports restoration and regulatory planning and decision making.
This geodatabase contains several feature classes depicting the historical ecological conditions of the Petaluma River Watershed in the late 1700s to late 1800s. This dataset integrates many sources of data describing the historical
landscape features. Extensive supporting information, including bibliographic references, analyses, and research methods, can be found
in the associated report:
SFEI has invested in novel, cost-effective solutions to costly problems. Most recently, our work with drones or Unmanned Aerial Systems (UAS) has yielded very promising results. We have used UAS to address a number of scientific challenges and use cases. SFEI applications of UAS include, wetland monitoring, restoration monitoring, sediment volume estimations, and trash surveys leveraging machine learning algorithms. In the course of our use of UAS, we have derived some useful analysis on the technology.
These datasets depict the historical habitat types and channel alignment of central Laguna de Santa Rosa and surrounding tributaries, representing average dry-season conditions prior to substantial Euro-American modification (~late 1700s-late 1800s). The data were also used to compare historical and current channel lengths as well as wetland and riparian extents.
This study synthesizes a diverse array of data to examine the ecological patterns, ecosystem functions, and hydrology that characterized a central portion of the Laguna de Santa Rosa during the mid-19th century, and to analyze landscape changes over the past 150 years. The primary purpose of this study was to help guide restoration actions and other measures aimed at reducing nutrient loads within this portion of the Laguna de Santa Rosa watershed.
Eelgrass (Zostera marina and Z. pacifica) is recognized as an important ecological resource in nearshore open coast areas, shallow bays, and estuaries throughout coastal California. Access to regional maps and related monitoring reports for eelgrass is crucial to monitor the extent of eelgrass habitat and how it is changing over time, evaluate the effects of coastal development projects on eelgrass habitat, and inform interested stakeholders and the public about eelgrass distribution.
This dataset includes reconstructed habitat types and ecological characteristics of the Tijuana River valley prior to substantial Euro-American modification (circa 1850). Documentation of historical ecological conditions is intended to serve as a tool to help support and guide restoration design, planning, and management of the river valley in the U.S. and Mexico.
Orthorectified historical aerial photography for the Petaluma River watershed was developed as a historical reference tool. The historical aerial photography mosaic was used to develop a reconstruction of the historical landscape and prevailing conditions of over approximately 150 square mile Petaluma River watershed. This dataset was developed to provide information for watershed management, the restoration of habitats, flood protection, and local education and research.
Orthorectified historical aerial photography for the San Joaquin River corridor was developed as a historical reference tool. The historical aerial photography mosaic was used to develop a reconstruction of the historical landscape and prevailing conditions of San Joaquin River corridor. This dataset was developed to provide information for watershed management, the restoration of habitats, flood protection, and local education and research.
This dataset contains information on the supply of sediment to major flood control channels around San Francisco Bay and the amount of sediment storage and removal over the past 50+ years. These data can also be explored in an interactive web map.
SediMatch is a web tool for matching restoration projects that need sediment with navigational and flood protection dredging projects and other "sediment suppliers" throughout the region to meet current and future sediment supply needs.
The San Francisco Bay Shore Inventory: Mapping for Sea Level Rise dataset provides a comprehensive and consistent picture of the 2016 Bay shore (up to MHHW + 10ft) for all nine Bay Area counties. The mapping captures features which affect flooding and flood routing (e.g., engineered levees, berms, embankments, roads, wetlands, etc.) including accredited and non-accredited structures. This project also identifies features fronted by wetlands and beaches and features that are artificially hardened (e.g., riprap).
Orthorectified historical aerial photography for the lower Laguna de Santa Rosa watershed was developed as a historical reference tool. The historical aerial photography mosaic was used to develop a reconstruction of the historical landscape and prevailing conditions of lower Laguna de Santa Rosa watershed. This dataset was developed to provide information for watershed management, the restoration of habitats, flood protection, and local education and research.
California's EcoAtlas provides access to project tracking 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.
This dataset includes reconstructed habitat types and ecological characteristics of the Novato Creek Baylands, representing average dry-season conditions prior to substantial Euro-American modification (~late 1700s-late 1800s). Documentation of historical ecological conditions is intended to serve as a tool to help support and guide wetland restoration and flood risk management along lower Novato Creek.
Orthorectified historical aerial photography for portions of the Dry Creek watershed, Sonoma County was developed as a historical reference tool. A total of 21 Aerial photos from 1942 were scanned and orthorectified. This dataset was developed to provide information for watershed management, the restoration of habitats, flood protection, and local education and research.
Satellite remote sensing will aid the State of California in assessing cyanobacterial bloom threats to animal and human health across the state’s numerous large lakes.
Georeferenced copies of all 42 T-sheets and associated stream and wetland vector data
GIS mapping of aquatic resources for the Laguna De Santa Rosa valley basin. This mapping effort represents a demonstration of the North Coast Aquatic Resource Inventory (NCARI) mapping standards. This data has been incorporated into CARI.
Please view the NCARI SOP for more information about NCARI mapping methods.
This historical aerial photography mosaic was used to develop a reconstruction of the historical landscape and prevailing conditions of Napa Valley. The early aerial photography from 1940 and 1942 was one of several data sources used to determine conditions prior to Euro-American modification. A small portion of one image from 1953 was used near St. Helena. The mosaic consists of early black and white aerial photography. 82 photographic prints covering the project area were obtained from the Napa County Resource Conservation District/Natural Resources Conservation Service.
The Bay Area EcoAtlas is a computer-based Geographic Information System (GIS) of past and present local ecology in the San Francisco Bay Area, California. It was designed to support local and regional environmental planning and management. The EcoAtlas represents the integration of many kinds of information from numerous sources, to compile a picture of the environmental past, the present, and change. It provided the most detailed regional views of past and present ecological conditions that were available at the time of creation.
Bay Area Aquatic Resources Inventory (BAARI) is a detailed base map of the Bay Area's aquatic features that includes wetlands, open water, streams, ditches, tidal marshes and flats, and riparian areas. BAARI was developed using a Geographic Information System (GIS) with true color imagery and a suite of ancillary data sources to consistently map aquatic resources around the Bay Area. The draft GIS dataset was extensively reviewed by regional wetland scientists and stakeholders to ensure it is as accurate as possible.
This visualization tool facilitates intuitive comparison of continuous data from around the Bay, and across a variety of analytes, to demonstrate the potential for collaborative monitoring across programs.
GreenPlan-IT is a versatile open-source toolset that helps aid municipalities with their efforts to plan and evaluate the placement of green infrastructure in the landscape and track the effectiveness of these installations in reducing stormwater run-off, PCB, and mercury in receiving waters.
The Riparian Zone Estimator Tool (RipZET) is a decision support tool developed by the San Francisco Estuary Institute and Aquatic Science Center for the California Riparian Habitat Joint Venture and the California Water Resources Control Board to assist in the visualization and characterization of riparian areas in the watershed context.
Web services provide a standard way to access geo-referenced data online. Although potential uses are numerous, typically web services allow one machine to exchange data with another for timely, automated, and efficient sharing of information. Different service types provide different levels of access to the data, including serving image tiles of the data or the features and attributes themselves.
SFEI is one of the state's Regional Data Centers that exchanges water quality data to the California Environmental Data Exchange Network (CEDEN). SFEI provides data management and visualization services to the San Francisco Bay-Delta and northern montane regions.
Fish and shellfish are nutritious and good for you to eat. But some fish and shellfish may take in toxic chemicals from the water they live in and the food they eat. Some of these chemicals build up in the fish and shellfish - and in the humans that eat fish and shellfish - over time. Although the chemical levels are usually low, it is a good idea to learn about advisories and monitoring in water bodies where you fish, and for fish or shellfish you eat.
Contaminant Data Display and Download Tool or CD3 is an innovative visualization tool for accessing water quality data for the San Francisco Bay-Delta and northern montane regions. It is the primary tool for accessing and downloading the San Francisco Bay Regional Monitoring Program’s (RMP) long-term dataset and other project data stored in SFEI's Regional Data Center
This report synthesizes historical evidence into a picture of how Coyote Creek looked and functioned before intensive modification. Prepared for the Santa Clara Valley Water District, the report helps explain contemporary landscape conditions and identify options for watershed restoration, natural flood protection, and integrated water management.