The San Francisco Bay and Sacramento–San Joaquin Delta Estuary — the Bay-Delta — is the largest estuary on the West Coast. The U.S. Geological Survey, the Interior Department's science agency, has long studied it with partners from federal, state and local government, universities and nonprofits. A USGS fact sheet sums up its recent work, mostly from the previous five years.
A tidal freshwater marsh of tules (Schoenoplectus acutus) in the Delta, with Mount Diablo behind. Photo: Judith Z. Drexler, U.S. Geological Survey.
Why it matters
| Area | More than 1,600 square miles |
| Watershed | More than 75,000 square miles — over 40% of California |
| People nearby | About 10 million |
| Species supported | More than 800 plants and animals |
| Water supplied | More than 27 million Californians and 4 million acres of Central Valley farmland |
Its waterways are the hub of California's freshwater delivery system. USGS supports the Delta Stewardship Council's lead scientist, who runs the Delta Science Program and the Delta Science Plan, updated every five years, and helps host the biennial Bay-Delta Science Conference. Its data are public and used by agencies from the Bureau of Reclamation and Army Corps of Engineers to the California Department of Water Resources.
Water flow and quality
A network of real-time monitoring stations, recording every 15 minutes, measures water level, flow, temperature, salinity, turbidity, pH, oxygen, chlorophyll, plankton, dissolved organic matter, nitrate, light and fish movement. Its data help agencies meet the flow and salinity rules that protect endangered fish, drinking water and supply. Boat sampling from the Lower South Bay to Rio Vista has run since 1969, and boats with flow-through sensors map water quality second by second.
USGS also studies pesticides used in Delta cities and farms, feeding state decisions under the Clean Water Act, and is mapping forms of mercury in the South Bay — including methylmercury, toxic to people and wildlife — from satellites, ships and water samples.
Harmful algal blooms occur in the Bay-Delta's fresh and salt water, fed by nutrient-rich wastewater, drought and water management. Their toxins can sicken or kill fish, marine mammals and birds and cause people anything from skin irritation to pneumonia or neurological problems. USGS tracks plankton, toxins and bloom genetics, is helping build a new regional monitoring strategy, and aims to forecast blooms.
A bloom of the cyanobacterium Dolichospermum at Franks Tract State Recreation Area in the Delta, August 3, 2022. Image from the USGS fact sheet on the Bay-Delta.
Fish and wildlife
- Imperiled fish. Studies of delta smelt, Chinook salmon, longfin smelt and Central Valley steelhead include a bioacoustic fish fence to protect young salmon and steelhead, tracking of green sturgeon during flood-control construction, and a "physics to fish" approach that has shown ways to improve habitat needing little or no extra water.
- Bird tracking. The Automated Interactive Monitoring System for Wildlife (AIMS) follows 25 bird species by GPS in real time — more than 75,000 hourly locations from 1,042 birds from January 2015 to February 2025 — and fed a model predicting the spread of highly pathogenic avian influenza in wild waterfowl. The tracks show California's flyway linked to the Great Basin and Great Salt Lake.
- Mercury. USGS set methylmercury toxicity reference values for many Central Valley and Bay-Delta birds, and linked prior bird flu infection to greater mercury toxicity in wild ducks.
- Nesting birds. In the South Bay, nests of American avocets, black-necked stilts and Forster's terns declined from 2005 to 2019, likely because of conversion to tidal marsh and the increased predation that followed.
*Figure 5.The U.S. Geological Survey collects multiple age classes of longfin smelt (Spirinchus thaleichthys) from Suisun Bay, California, to increase knowledge about life history and provide
inputs for future population modeling. This information is used by the U.S. Army Corps
of Engineers to guide.*
GPS tracks of marked waterbirds, 2015–2025, from the AIMS system. Image from the USGS fact sheet on the Bay-Delta.
Wetland restoration
Since the Gold Rush, 85% of the Bay's wetlands and 98% of the Delta's have been converted to other uses, costing flood control and habitat. Restoration programs — the South Bay Salt Ponds Project, California EcoRestore, Proposition 1 and Measure AA — are bringing some back. USGS measures how fast restored marshes gain elevation, how sediment and vegetation develop, and whether they support endangered species. With the Army Corps and the Port of Redwood City, it is testing placing dredged sediment where waves and currents will carry it onto marshes. At the 1,200-acre Dutch Slough restoration, and at Rush Ranch in Suisun Marsh since 2014, it tracks how much carbon wetlands store.
*Figure 8.The Dutch Slough Tidal Wetland Restoration, led by the California Department of Water
Resources, is being used as a living laboratory to study wetland restoration processes.
U.S. Geological Survey researchers have measured carbon dynamics over vegetation,
soil, and open water using A, a las.*
Researchers measure tiny changes in marsh elevation with a sedimentation erosion table at Rush Ranch, February 2025. Image from the USGS fact sheet on the Bay-Delta.
Invasive species
- Invasive clams — Amur River clams and Asian clams — strip phytoplankton from the base of the food web. Salinity largely controls them, suggesting managed flows could keep them down.
- Brazilian waterweed, infesting the Delta for more than 70 years, traps sediment before it reaches tidal marshes, weakening them.
- Water primrose releases a toxic "tea" through its leaves, which probably helps it crowd out native tule marsh.
Hazards
- Floods and rising seas. The Coastal Storm Modeling System (CoSMoS) forecasts coastal flooding, erosion and rising groundwater under sea-level and storm scenarios, as California swings between drought and flood.
- Marsh futures. The Coastal Wetland Equilibrium Model projects whether Delta marshes can keep up with sea-level rise. USGS also assessed three ways to store more carbon: restoring managed wetlands, targeted farm water management, and returning tides to wetlands.
- Landslides. Steep hills and heavy winter rain make the Bay Area landslide-prone. USGS works with the National Weather Service on soil-moisture monitoring to warn of fast-moving debris flows, and new lidar of the whole Bay-Delta, captured in summer 2025, will sharpen maps of landslides, floods, faults and tsunamis.
- Wildfire. Studies focus on aftermath — vegetation recovery, landslide risk, contaminants and water quality. One found wetland vegetation recovered quickly after fire without changing species makeup.
- Earthquakes. The Northern California Seismic Network watches constantly. The HayWired scenario modeled a magnitude 7.0 quake on the Hayward fault. In the Delta, quakes are rarer but could breach the levees protecting farms and the state's water system; a recent study mapped the region's active faults and how they move.
A landslide on Wildcat Canyon Road in Berkeley after atmospheric-river storms in January 2023. Image from the USGS fact sheet on the Bay-Delta.
Sources
Based on "Recent scientific contributions by the U.S. Geological Survey in the San Francisco Bay and Sacramento–San Joaquin Delta," U.S. Geological Survey Fact Sheet 2025–3058; a work of the United States government in the public domain. Pictures an earlier version of this page left out were restored on 2026-09-26.
Licence: CC0 1.0 (public domain) · Adapted from pubs.usgs.gov
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