Ecosystem Restoration in San Francisco Bay and Delta

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In many systems, particularly the relatively dry western United States, freshwater that historically flowed into estuaries has been diverted for drinking water, agriculture, and industry. The resulting changes to water flow profoundly altered estuarine ecosystems. CMHRP studies in this complex system inform resource managers tasked with balancing conflicting needs for water and restoration of critical estuarine and wetland ecosystems.

Video Transcript

What is the Delta? This short video is intended to serve as an introduction to the Sacramento-San Joaquin Delta, and is the first in a series of four short videos highlighting USGS science in the San Francisco Bay and Sacramento-San Joaquin Delta estuary. This video orients the viewer to physical characteristics of the delta, the challenges facing it, and the work the USGS is doing, in coordination with our partners, to understand and characterize the delta ecosystem. Credit: Stephen M. Wessells, USGS » View the video

The San Francisco estuary, California, composed of San Francisco Bay and the Sacramento-San Joaquin Delta, is the largest estuary on the West Coast. It supports a diverse and productive ecosystem as well as economic activities such as shipping, recreation, and sand mining. Freshwater flowing into the delta is diverted for agricultural and municipal water supplies. Water diversions affect the estuarine ecosystem by altering the salinity gradient from fresh to marine waters. This ecosystem also faces many other threats due to urbanization and climate change, presenting complex management challenges. Large-scale ecosystem restoration, predominantly of tidal marsh, is underway in the bay and delta. 

A woman and a man stand on the stern of a boat wearing safety gear, man is pressing on a piece of equipment.

Dan Powers (USGS) and Rachel Marcuson (USGS) prepare to deploy a Gomex sediment corer from R/V Snavely in the Mokulumne River near confluence of San Joaquin River in the Sacramento-San Joaquin Delta, California. Credit: J.R. Lacy, USGS

A man stands near a tripod with an instrument on it, he is wearing field gear like hip waders, steel toed boots, field vest.

Josh Logan (USGS) surveys position and elevation of instrumentation to measure water level and suspended-sediment concentration in the marsh at China Camp State Park in Marin County, California, adjacent to San Pablo Bay (northern San Francisco Bay). Credit: J.R. Lacy, USGS

The CMHRP is involved in numerous projects in the San Francisco estuary, from habitat conservation, restoration, and resilience, to understanding the effects of sea level rise. CMHRP scientists study sediment transport in the estuary and how Earth processes and human intervention shaped the estuary, and contribute expertise on physical processes to collaborative interdisciplinary projects. Below we describe two of our projects.

Sediment Delivery to Marches

Marshes occupy a narrow range of elevations relative to sea level, and they maintain elevation as sea level rises by accumulating sediment transported from adjacent waters. The success of many marsh restoration projects depends upon sediment accretion keeping pace with sea level rise, but the dynamics that deliver sediment to marshes are poorly understood. The CMHRP is studying sediment exchange between estuarine mudflats and fringing marshes at China Camp State Park in northern San Francisco Bay. CMHRP scientists measure sediment flux in tidal creeks within the marsh, wave and suspended-sediment properties in bay shallows, and wave attenuation and sediment trapping at the marsh edge. Results from the China Camp study will improve predictive models of marsh accretion and management of marshes threatened by sea level rise. This project is a collaboration with the San Francisco Bay National Estuarine Research Reserve.

Two women stand on the stern of a boat, they are wearing hard hats, life jackets, steel-toed boots, maneuvering an apparatus.

Jenny White (USGS) and Lissa MacVean (USGS) deploy an instrumented frame in the shallows of San Pablo Bay (northern San Francisco Bay) from R/V Retriever. The instrument is an acoustic Doppler current profiler. Credit: J.R. Lacy, USGS

Delta Smelt being held in hand

Delta smelt being displayed on a hand. Credit: National Geographic Society

Drivers of Aquatic Habitat

Water export from the San Joaquin Delta is managed by Federal (U.S. Bureau of Reclamation, USBR) and state agencies. These large water projects must be managed both to provide water reliably and to protect species of concern. Fisheries are in decline in the San Joaquin Delta, and several species, including the delta smelt, are threatened or endangered. Major habitat restoration efforts are planned to benefit delta smelt and other native fish species; however, the optimal physical habitat characteristics for these fish are not well understood. The CMHRP collaborates with the USGS Water Resources Mission Area in a USBR-supported study to address critical knowledge gaps about how shallow-water habitats support native fish species. The CMHRP investigates sediment dynamics (i.e., the motion of sediment), and the influence of wind waves on turbidity (the cloudiness of the water)—a habitat characteristic important to delta smelt—in two flooded agricultural tracts in the northern delta with different landscape configurations. Results will help guide ecosystem management actions, including flow manipulations and habitat restoration.

A small boat sits on calm waters with trees in the distance, and a cloudy sky.

Mokelumne River near confluence with the San Joaquin River in the Sacramento-San Joaquin Delta, California, looking downstream, with Cordell Johnson (USGS) and Rachel Allen (USGS) collecting data from R/V Fast Eddy. Credit: J.R. Lacy, USGS