The San Francisco Bay-Delta PES is one way that USGS continues to provide science for the restoration and conservation of the SF Bay and its watershed. USGS research topics range from wetland restoration in the Bay to restoring habitat for anadromous fish (e.g., salmon) in the uplands. USGS has made several important discoveries critical to the fundamental understanding of this system and continues to conduct critical work necessary to improve the restore of a system faced with multiple pressures including climate change. Within the PES we combine our capacities in the multiple disciplines necessary to conduct the research to provide information needed by decision makers across various agencies.
San Francisco Bay-Delta Research
Avian Ecology and Multi-Species Habitat Use in Pacific Coast Estuaries
Ecological Effects of Contaminants
Waterbird Breeding Ecology and Management
Contaminants in Waterbirds and Effects on Avian Reproduction
Mercury Bioaccumulation in Wetlands
Modeling Sea-Level Rise in San Francisco Bay Estuary
Ecology and Population Dynamics of Ridgway's Rails along the West Coast of the U.S.
Wetland Restoration in the San Francisco Bay Delta and Pacific Northwest
Coastal Ecosystem Response to Sea-level Rise
Ecological Stressors - Rocky Coastlines, Mangroves, Marshes, Droughts, and Storms
Reproductive Success of Black-Crowned Night-Herons and Snowy Egrets on Alcatraz Island
Food Web and Invertebrate Ecology Studies in Pacific Coast Estuaries
Recent data (2020-2022) related to USGS San Francisco Bay-Delta research are listed below. A complete listing of USGS San Francisco Bay-Delta data is available from the button below.
Surface Elevation Table Measurements at Five Tidal Marshes Across the San Francisco Bay-Delta (2016-2019)
Annual Marbled Murrelet Abundance and Productivity Surveys Off Central California (Zone 6), 1999-2021 (ver. 4.0, May 2022)
Growth and Capture-Mark-Recapture Data for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia, in San Mateo County, California from 2007 to 2020
Tidal Wetland Elevation Projections for Five San Francisco Bay Delta Regions Using WARMER-2, 2000-2100
Breeding Waterbird Populations in South San Francisco Bay 2005-2019
WARMER-2 Model Inputs and Projections for Three Tidal Wetland Sites Across San Francisco Bay Estuary
Sediment biogeochemistry and subsequent mercury biomagnification in wetland food webs of the San Francisco Bay, CA
Western sandpiper diet composition in south San Francisco Bay, CA
Priority Ecosystem Science Program: benthic community and bivalve metrics data in Grizzly Bay and San Pablo Bay (2019-20)
Impounded and tidal wetland plant diversity and composition across spatial scales, San Francisco Bay-Delta, California, USA (2016-2018)
Small mammal surveys from northern San Francisco Bay: 1998-2014
Recent publications (2020-2022) related to USGS San Francisco Bay-Delta research are listed below. A complete listing of USGS San Francisco Bay-Delta publications is available from the button below.
Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries
Abundance and productivity of Marbled Murrelets (Brachyramphus marmoratus) off central California during the 2020 and 2021 breeding seasons
Abundance and productivity of Marbled Murrelets (Brachyramphus marmoratus) off central California during the 2020 and 2021 breeding seasons
Atmospheric river storm flooding influences tidal marsh elevation building processes
Keeping an eye on water quality from the sky
Small shorebirds feast on green slime to fuel their long migration
Incorporation of uncertainty to improve projections of tidal wetland elevation and carbon accumulation with sea-level rise
Breeding waterbird populations have declined in south San Francisco Bay: An assessment over two decades
An integrated population model for southern sea otters
Effects of season, location, species, and sex on hematologic and plasma biochemical values and body mass in free-ranging Grebes (Aechmophorus species)
Distribution, abundance, and genomic diversity of the endangered antioch dunes evening primrose (Oenothera deltoides subsp. howellii) surveyed in 2019
Waterfowl use of wetland habitats informs wetland restoration designs for multi‐species benefits
Explore our research using the web tools listed below.
Re-establishing Waterbird Breeding Colonies in San Francisco Bay
This U.S. Geological Survey (USGS), Western Ecological Research Center (WERC) story map details how partners are using science and management to maintain and establish new bird nesting colonies in support of the South Bay Salt Pond Restoration Project. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
- Overview
The San Francisco Bay-Delta PES is one way that USGS continues to provide science for the restoration and conservation of the SF Bay and its watershed. USGS research topics range from wetland restoration in the Bay to restoring habitat for anadromous fish (e.g., salmon) in the uplands. USGS has made several important discoveries critical to the fundamental understanding of this system and continues to conduct critical work necessary to improve the restore of a system faced with multiple pressures including climate change. Within the PES we combine our capacities in the multiple disciplines necessary to conduct the research to provide information needed by decision makers across various agencies.
San Francisco Bay-Delta ResearchAvian Ecology and Multi-Species Habitat Use in Pacific Coast Estuaries
Waterbirds such as shorebirds, waders, and ducks depend on healthy and productive estuaries to “fuel up” for long distance migrations along the Pacific Flyway. Estuarine ecosystems include a mosaic of managed, natural, and restoring wetlands, and provide critical stop-over and wintering areas for federally protected migratory bird species. USGS WERC’s Dr. Susan De La Cruz works with federal, state...Ecological Effects of Contaminants
Whereas the other themes of the Contaminant Ecology Research Program focus on where, why, and how contaminants cycle and bioaccumulate in ecological systems, this theme is focused on determining what happens at environmentally relevant concentrations.Waterbird Breeding Ecology and Management
The San Francisco Bay is designated as a site of hemispheric importance to shorebirds and annually supports over one million waterbirds. Within the USGS WERC waterbird breeding ecology program, Dr. Josh Ackerman and partners are studying habitat selection, movements, and factors influencing waterbird nest success and chick growth and survival.Contaminants in Waterbirds and Effects on Avian Reproduction
California’s Central Valley and San Francisco Bay Estuary have a long history of mercury contamination from past mercury mining and gold extraction. Waterbirds are particularly susceptible to mercury because of their use of wetland habitats where methylmercury (the most toxic and biologically available form) is produced and relatively low methylmercury exposure can reduce reproductive success...Mercury Bioaccumulation in Wetlands
Wetlands provide numerous ecosystem services, but also can be sources of methylmercury production and export. Click the next tab to learn how WERC's Dr. Josh Ackerman is evaluating the ecological factors that drive contaminant bioaccumulation in wetland-dependent fish and wildlife.Modeling Sea-Level Rise in San Francisco Bay Estuary
With sea level rise, how will the coastal habitats of the San Francisco Bay Estuary change over the next 100 years? Mapping and modeling studies by Dr. Karen Thorne, WERC scientists, and partners have produced scenarios for this important coastal ecosystem.Ecology and Population Dynamics of Ridgway's Rails along the West Coast of the U.S.
The Ridgway’s rail is a federal and state listed endangered species that occurs in wetlands along the Pacific Coast and from the Lower Colorado River drainage to southern Baja California. Three subspecies of Ridgway’s rail are found within the United States: the California Ridgway’s Rail, Yuma Ridgway’s rail, and Light-footed Ridgway’s rail. All three subspecies have declined since 1900 as a...Wetland Restoration in the San Francisco Bay Delta and Pacific Northwest
Estuaries and healthy coastal habitats are among the most productive ecosystems on Earth. They provide a variety of benefits, including habitat and food for fish and wildlife, flood and erosion protection, improved water quality, increased carbon sequestration, as well as beautiful scenery and opportunities for recreation. Along the U.S. Pacific Coast, both the San Francisco Bay estuary and the...Coastal Ecosystem Response to Sea-level Rise
USGS WERC’s Dr. Karen Thorne, her team of reseachers, and her partners are currently taking a local site network approach to describe current and future conditions and projected responses of coastal ecosystems to sea-level rise and other stressors. The Coastal Ecosystem Response to Climate Change (CERCC) program’s goal is to understand how ecosystems vary in their ability to keep up with sea-level...Ecological Stressors - Rocky Coastlines, Mangroves, Marshes, Droughts, and Storms
Coastal estuaries that contain marshes and mangroves are currently being reshaped by changing ocean and atmospheric conditions through prolong drought, sea-level rise and increased extreme storm events. Many projected increases in sea-level are expected to result in loss of tidal wetlands and their component species. In addition, changing sediment loads, extreme tide and storm events, and shifting...Reproductive Success of Black-Crowned Night-Herons and Snowy Egrets on Alcatraz Island
Years after the last inmate departed Alcatraz Island, waterbirds like Black-crowned Night Herons and Snowy Egrets still make the forbidding island their home. The National Park Service has requested the aid of WERC’s Dr. Pete Coates to inform efforts to expand visitor access to the Island, and simultaneously maintain healthy waterbird populations.Food Web and Invertebrate Ecology Studies in Pacific Coast Estuaries
Invertebrate communities provide food for several economically and ecologically important fish and waterbird species in coastal estuaries. Scientists at the WERC San Francisco Bay Estuary Field Station specialize in studying foraging ecology of waterbirds and fishes, general food web dynamics across estuaries, and the effects of habitat restoration and other factors on waterbird prey availability. - Data
Recent data (2020-2022) related to USGS San Francisco Bay-Delta research are listed below. A complete listing of USGS San Francisco Bay-Delta data is available from the button below.
Surface Elevation Table Measurements at Five Tidal Marshes Across the San Francisco Bay-Delta (2016-2019)
Surface elevation tables with marker horizons (SET-MH) measure millimeter-scale changes in elevation over time. A combination of pin measurements (elevation change) and surface deposition measurements (marker horizon) is used to distinguish elevation changes due to belowground and aboveground processes. SET-MHs were installed in 2016 and were measured quarterly across five tidal marshes (PetalumaAnnual Marbled Murrelet Abundance and Productivity Surveys Off Central California (Zone 6), 1999-2021 (ver. 4.0, May 2022)
Since 2017, U.S. Geological Survey, Western Ecological Research Center (USGS WERC) partnered with California State Parks to continue long-term, annual at-sea surveys to estimate at-sea abundance and juvenile (i.e. hatch-year) productivity of Marbled Murrelets (Brachyramphus marmoratus) in U.S. Fish and Wildlife Service Conservation Zone 6 (central California: San Francisco Bay to Monterey Bay). MaGrowth and Capture-Mark-Recapture Data for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia, in San Mateo County, California from 2007 to 2020
This dataset includes records of captures of San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) collected at five sites from 2007 to 2020. The data include measurements of snake snout-vent length to estimate growth patterns, snake sex, and the record of all captures of individual snakes for estimating capture probability, availability for capture, and survival. These data support the foTidal Wetland Elevation Projections for Five San Francisco Bay Delta Regions Using WARMER-2, 2000-2100
Projections of marsh elevation change with WARMER-2 across five regions of the San Francisco Bay Delta (Cache Yolo, South Delta, North Delta, Central Delta, and Suisun). The model was run across a range of initial elevations for each region and for scenarios of sea-level rise (30, 61, 91, 122, 152, 183, 305 cm by 2100), sediment availability (historic, constant, declining, and increase), and withBreeding Waterbird Populations in South San Francisco Bay 2005-2019
The dataset includes three separate excel spreadsheets which provides waterbird (and predator) observations within individual survey units during the May 2019 breeding waterbird survey of south San Francisco Bay (2019WaterbirdSurveyFullData.xlsx), the total number of American avocets, black-necked stilts, and Forster's terns within each pond unit surveyed during the May 2019 survey (2019WaterbirdSWARMER-2 Model Inputs and Projections for Three Tidal Wetland Sites Across San Francisco Bay Estuary
Understanding the rates and patterns of tidal wetland elevation changes relative to sea-level is essential for understanding the extent of potential wetland loss over the coming years. Using an enhanced and more flexible modeling framework of an ecosystem model (WARMER-2), we explored sea-level rise (SLR) impacts on wetland elevations and carbon sequestration rates through 2100 by considering planSediment biogeochemistry and subsequent mercury biomagnification in wetland food webs of the San Francisco Bay, CA
Methylmercury (MeHg) is a globally pervasive contaminant that biomagnifies in food webs and can reach toxic concentrations in consumers at higher trophic levels, including wildlife and humans. The production of MeHg, and its subsequent entry and biomagnification in food webs, is governed by a complex suite of biogeochemical, physical, and ecological processes, resulting in variation in the distribWestern sandpiper diet composition in south San Francisco Bay, CA
Diet composition can be influenced by age- and sex-related factors including an individual's morphology, social status, and acquired skills; however, specialization may only be necessary when competition is intensified by high population densities or increased energetic demands. The western sandpiper is a small (22-35 grams) migratory shorebird that exhibits female-biased sexual size dimorphism wiPriority Ecosystem Science Program: benthic community and bivalve metrics data in Grizzly Bay and San Pablo Bay (2019-20)
Sediments and sediment transport influence the physical habitat and the ecology of the San Francisco Bay estuary. Bed sediments provide habitat for benthic organisms and the transport of sediment transports nutrients and contaminants throughout the San Francisco Bay. As part of the SF Bay-Delta Priority Ecosystems Science Program project: Biophysical Controls on Erosion and Near-Bed Turbulence: StImpounded and tidal wetland plant diversity and composition across spatial scales, San Francisco Bay-Delta, California, USA (2016-2018)
These datasets provide information on plant alpha, beta, and gamma diversity, and plant species abundance at several spatial scales for tidal wetlands along a salinity gradient in the San Francisco Bay-Delta and an impounded brackish wetland complex in Suisun Marsh, California. Files include diversity metrics calculated at the patch, site, and region scales, average percent cover of wetland dominaSmall mammal surveys from northern San Francisco Bay: 1998-2014
This datasets summarizes small mammal trapping efforts that USGS San Francisco Bay Estuary Field Station has led, co-led, or supervised, to detect and monitor the endangered salt marsh harvest mouse (Reithrodontomys raviventris) in the northern reaches of San Francisco Bay from 1998-2014. As the salt marsh harvest mouse is listed as endangered under the Endangered Species Act, sensitive location - Multimedia
- Publications
Recent publications (2020-2022) related to USGS San Francisco Bay-Delta research are listed below. A complete listing of USGS San Francisco Bay-Delta publications is available from the button below.
Filter Total Items: 21Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries
Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, anAuthorsRaman P. Nagarajan, Mallory Bedwell, Ann E. Holmes, Thiago Sanches, Shawn Acuña, Melinda R. Baerwald, Matthew A. Barnes, Scott Blankenship, Richard E. Connon, Kristy Deiner, Daphne Gille, Caren S. Goldberg, Margaret Hunter, Christopher L. Jerde, Gordon Luikart, Rachel S. Meyer, Alison Watts, Andrea M SchreierAbundance and productivity of Marbled Murrelets (Brachyramphus marmoratus) off central California during the 2020 and 2021 breeding seasons
Marbled murrelets (Brachyramphus marmoratus) have been listed as “endangered” by the State of California and “threatened” by the U.S. Fish and Wildlife Service since 1992 in California, Oregon, and Washington. Information regarding marbled murrelet abundance, distribution, population trends, and habitat associations is critical for risk assessment, effective management, evaluation of conservationAuthorsJonathan J. Felis, Josh Adams, Cheryl Horton, Emily C. Kelsey, Laney M. WhiteAbundance and productivity of Marbled Murrelets (Brachyramphus marmoratus) off central California during the 2020 and 2021 breeding seasons
Marbled murrelets (Brachyramphus marmoratus) have been listed as “endangered” by the State of California and “threatened” by the U.S. Fish and Wildlife Service since 1992 in California, Oregon, and Washington. Information regarding marbled murrelet abundance, distribution, population trends, and habitat associations is critical for risk assessment, effective management, evaluation of conservationAuthorsJonathan J. Felis, Josh Adams, Cheryl Horton, Emily C. Kelsey, Laney M. WhiteAtmospheric river storm flooding influences tidal marsh elevation building processes
Disturbances are a key component of ecological processes in coastal ecosystems. Investigating factors that affect tidal marsh accretion and elevation change is important, largely due to accelerating sea-level rise and the ecological and economic value of wetlands. Sediment accumulation rates, elevation change, and flooding were examined at five marshes along a riverine-tidal gradient in the northeAuthorsKaren M. Thorne, Scott Jones, Chase M. Freeman, Kevin J. Buffington, Christopher N. Janousek, Glenn R. GuntenspergenKeeping an eye on water quality from the sky
You can learn a lot about rivers, lakes, estuaries, and oceans by looking down at them from the sky. Scientists use a technique called remote sensing to measure the amount of light or heat energy reflected and emitted from the Earth. Sensors can be on satellites or mounted on airplanes, helicopters, or drones. Scientists use this information to map the quality of water in the San Francisco Bay-DelAuthorsFrancine H. Mejia, Christian E. Torgersen, Cédric G FichotSmall shorebirds feast on green slime to fuel their long migration
Shorebirds wade in shallow waters along shorelines searching for food. More than a million shorebirds visit the San Francisco Estuary each year during their migration to feast on the insects, worms, clams, and crabs that live on or under the surface of the sand or mud. The abundant food in the Estuary provides shorebirds with the energy they need to migrate thousands of kilometers, between their bAuthorsLaurie Anne Hall, Susan E. W. De La Cruz, Isa Woo, Tomohiro Kuwae, David Mcgovern Nelson, John Y. TakekawaIncorporation of uncertainty to improve projections of tidal wetland elevation and carbon accumulation with sea-level rise
Understanding the rates and patterns of tidal wetland elevation changes relative to sea-level is essential for understanding the extent of potential wetland loss over the coming years. Using an enhanced and more flexible modeling framework of an ecosystem model (WARMER-2), we explored sea-level rise (SLR) impacts on wetland elevations and carbon sequestration rates through 2100 by considering planAuthorsKevin J. Buffington, Christopher N. Janousek, Bruce D. Dugger, John C. Callaway, Lisa Schile-Beers, Evyan Borgnis Sloane, Karen M. ThorneBreeding waterbird populations have declined in south San Francisco Bay: An assessment over two decades
In south San Francisco Bay, former salt ponds now managed as wildlife habitat support large populations of breeding waterbirds. In 2006, the South Bay Salt Pond Restoration Project began the process of converting 50% to 90% of these managed pond habitats into tidal marsh. We compared American Avocet (Recurvirostra americana) and Black-necked Stilt (Himantopus mexicanus) abundance in south San FranAuthorsC. Alex Hartman, Josh T. Ackerman, Carley Rose Schacter, Mark P. Herzog, Max Tarjan, Yiwei Wang, Cheryl Strong, Rachel Tertes, Nils WarnockAn integrated population model for southern sea otters
Southern sea otters (Enhydra lutris nereis) have recovered slowly from their near extinction a century ago, and their continued recovery has been challenged by multiple natural and anthropogenic factors. Development of an integrated population model (IPM) for southern sea otters has been identified as a management priority, to help in evaluating the relative impacts of known threats and guide bestAuthorsM. Tim Tinker, Lilian P. Carswell, Joseph A. Tomoleoni, Brian B. Hatfield, Michael D. Harris, Melissa A. Miller, Megan E. Moriarty, Christine K. Johnson, Colleen Young, Laird A. Henkel, Michelle M. Staedler, A. Keith Miles, Julie L. YeeEffects of season, location, species, and sex on hematologic and plasma biochemical values and body mass in free-ranging Grebes (Aechmophorus species)
The effects of season, location, species, and sex on body weight and a comprehensive array of blood chemistry and hematology analytes were compared for free-ranging western (Aechmophorus occidentalis) and Clark's (Aechmophorus clarkii) grebes. Birds (n = 56) were collected from Puget Sound, WA, and Monterey Bay and San Francisco Bay, CA, from February 2007 to March 2011. The data supported generalAuthorsNancy L Anderson, Susan E. W. De La Cruz, Joseph K Gaydos, Michael H. Ziccardi, Danielle J HarveyDistribution, abundance, and genomic diversity of the endangered antioch dunes evening primrose (Oenothera deltoides subsp. howellii) surveyed in 2019
Sand dune ecosystems are highly dynamic landforms found along coastlines and riverine deltas where a supply of sand-sized material is available to be delivered by aquatic and wind environments. These unique ecosystems provide habitat for a variety of endemic and rare plant and animal species. Sand dunes have been affected by human development, sand mining, and shoreline stabilization from invasiveWaterfowl use of wetland habitats informs wetland restoration designs for multi‐species benefits
Extensive global estuarine wetland losses have prompted intensive focus on restoration of these habitats. In California, substantial tracts of freshwater, brackish and tidal wetlands have been lost. Given the anthropogenic footprint of development and urbanization in this region, wetland restoration must rely on conversion of existing habitat types rather than adding new wetlands. These restoratioAuthorsMichael L. Casazza, Fiona McDuie, Scott Jones, Austen Lorenz, Cory T. Overton, Julie L. Yee, Cliff L. Feldheim, Josh T. Ackerman, Karen M. Thorne - Web Tools
Explore our research using the web tools listed below.
Re-establishing Waterbird Breeding Colonies in San Francisco Bay
This U.S. Geological Survey (USGS), Western Ecological Research Center (WERC) story map details how partners are using science and management to maintain and establish new bird nesting colonies in support of the South Bay Salt Pond Restoration Project. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.