Sacramento River Basin, California

The West Coast Region’s Sacramento River Basin Branch is located in the Central Valley Office in Sacramento, California

The West Coast Region’s Sacramento River Basin Branch is located in the Central Valley Office in Sacramento, California. The Branch has responsibility for Endangered Species Act (ESA)-listed salmon, steelhead, and green sturgeon conservation and recovery, north of the Sacramento/San Joaquin River Delta, including waters of the Sacramento River and its tributaries.

Suspension bridge crossing the Sacramento River

Sacramento River

The Sacramento River Basin is the largest watershed in the state of California, covering 27,000 square miles and carrying approximately 30% of the state’s total surface water. The Sacramento River boasts four distinct runs of Chinook salmon: fall-run, late fall-run, winter-run, and spring-run. Because of this diversity in run timing, the Sacramento River is occupied by Chinook salmon year-round. Other anadromous fish in the Sacramento River watershed include steelhead, green and white sturgeon, and lampreys.

A map of historic salmon habitat in the California Central Valley. Accessible habitat is colored blue, habitat inaccessible to fish due to dams is colored black. A majority of the watersheds are shaded black.

The Sacramento River and its tributaries have gone through many modifications in the last hundred years. Modifications include dams, water diversions, stream channelization, and mining. These habitat changes not only reduced the quantity of available habitat, but the quality is diminished as well. Changes in historic seasonal river flows affect the natural functions of the watershed, which can, in turn, affect survival of fish. In many areas, fish can no longer access historic spawning locations. Remaining available habitat is subject to warm water temperatures, poor water quality, and altered flows, which impacts egg survival, rearing, and migration.

As a result of these many factors, four types of anadromous fish have been identified as threatened or endangered under the Endangered Species Act. NOAA Fisheries manages conservation and promotes recovery of these species listed below.

  • Sacramento River (SR) winter-run Chinook salmon (endangered)
  • Central Valley (CV) spring-run Chinook salmon (threatened)
  • California Central Valley (CCV) steelhead trout (threatened)
  • Southern Distinct Population Segment (sDPS) green sturgeon (threatened)

Key rivers and creeks in the Sacramento River Basin include:

Feather River

Feather River

The Feather River is the largest tributary to the Sacramento River. It originates in the Sierra Nevada mountain range and flows 211 miles from its headwaters to Verona, where it meets the Sacramento River. Currently, only 64 miles of this habitat is available to anadromous fish. This includes the area downstream of Oroville Dam, where the watershed extends south and includes the drainage of the Yuba and Bear rivers. In the 1960s Oroville Dam was constructed for water supply, hydroelectric, and flood control purposes. It is the tallest dam in the country at 770 feet. Fish passage is blocked at the fish barrier weir adjacent to the Feather River Hatchery, a few miles downstream of Oroville Dam. Because Oroville Dam prevents migrating salmonids from reaching spawning and rearing habitat in the upper watershed, the Feather River Hatchery was established to supplement populations of Chinook salmon and steelhead. Hatchery production of Central Valley spring-run Chinook salmon is for conservation purposes with the goal of conserving genetic characteristics specific to Feather River spring-run Chinook salmon. Hatchery production of fall-run Chinook salmon is for mitigation, so that Chinook salmon can continue to be sustainably harvested both commercially and recreationally. The hatchery produces California Central Valley steelhead both for conservation and as mitigation to sustain California’s steelhead fishing opportunities.

Yuba River

Yuba River

The Yuba River, a tributary of the Feather River, historically supported the largest naturally-reproducing population of California Central Valley steelhead.

While it still supports a persistent population of California Central Valley steelhead, it is also known for being the location of some of the first hydroelectric dam projects in California. These dams, including Englebright Dam, New Bullards Bar Dam, and Daguerre Point Dam are currently undergoing Federal Energy Regulatory Commission (FERC) relicensing. The relicensing process creates an opportunity for improved fish passage around the dams allowing these native salmon to be reintroduced back into their habitat above the dams. After nearly 80 years, these fish may once again make the journey to spawn in the cold waters of the Upper Yuba River in their historic spawning grounds.

American River

American River

The American River empties into the Sacramento River at the City of Sacramento. With 125 miles of historic habitat, this tributary is the second largest contributor of flows to the Sacramento River. However, of those 125 miles, only 23 miles are available to anadromous fish. The other hundred-plus miles are behind Nimbus Dam and inaccessible to migrating salmonids. Nimbus Dam exists to regulate flow releases from Folsom Dam into the Lower American River. Folsom Dam was built primarily for flood control and also provides water storage for irrigation and hydroelectric purposes. Because the construction of these dams left such limited habitat for salmonids, the Nimbus Fish Hatchery was constructed. Operated by the California Department of Fish and Wildlife (CDFW) under contract with the United States Bureau of Reclamation (Reclamation), this hatchery produces fall-run Chinook salmon and California Central Valley steelhead as mitigation for above-dam habitat losses.

Clear Creek

Clear Creek

Clear Creek is the first major tributary to the Sacramento River below Shasta Dam. Whiskeytown Dam, constructed in 1963, stores and regulates water from the Clear Creek watershed and diversions from the Trinity River. Historically there were 25 river miles of salmon habitat accessible, currently 18.1 miles are accessible due to Whiskeytown Dam. Clear Creek has recently been the focus of many restoration efforts, such as channel and habitat restoration, gravel augmentation, riparian restoration, and management of instream flows. Central Valley spring-run Chinook salmon and California Central Valley steelhead populations in Clear Creek have responded positively to these extensive restoration efforts by joint agency partnerships.

Battle Creek

Battle Creek

Battle Creek contains the only remaining accessible habitat for endangered Sacramento River winter-run Chinook salmon other than the mainstem Sacramento. Winter-run has been identified by NOAA Fisheries as one of nine species most at risk of becoming extinct. Because of the habitat potential for recovery of ESA-listed salmonids, Battle Creek is undergoing major restoration, including dam removals and habitat enhancement. In 2016, after the drought claimed nearly two years worth of Sacramento River winter-run Chinook salmon offspring, a multi-agency team of biologists took action by jumpstarting the reintroduction of winter-run Chinook into Battle Creek. This effort proved to be a successful tool for addressing anticipated climate effects that threaten Sacramento River winter-run Chinook salmon.

Cottonwood Creek

Cottonwood Creek

Cottonwood Creek is the third largest tributary to the Sacramento River and the largest undammed tributary in the upper Sacramento River Basin. Cottonwood Creek contains populations of Central Valley spring-run Chinook and California Central Valley steelhead. However, under most conditions it does not contain suitable spawning habitat to support a Chinook salmon population. Beegum Creek, a tributary to Cottonwood Creek, does contain habitat for spawning and holding of Central Valley spring-run Chinook and supports a small persistent population of these fish. Populations in Cottonwood Creek are thought to be dependent on straying fish from nearby watersheds and the habitat and populations in Cottonwood Creek may serve to link other populations in a way that increases viability of ESA-listed salmonids over longer time scales.

Mill Creek

Mill Creek

Mill Creek is an eastside tributary to the Sacramento River that originates near a thermal spring area in Lassen Volcanic National Park (LVNP) at an elevation of approximately 8,200 feet. Mill Creek initially flows through meadows and dense forests in LVNP for an estimated 43 miles before descending rapidly through a steep rock canyon and flowing into the Sacramento Valley. Once Mill Creek reaches the valley, it flows for eight miles across the valley floor and converges with the Sacramento River. With the exception of impaired stream flows and fish passage conditions on the valley floor, habitat in the upper watershed is in good condition. Mill Creek contains Central Valley spring-run Chinook and California Central Valley steelhead. It is recognized as supporting one of three self-sustaining Central Valley spring-run Chinook salmon populations in the Sacramento River watershed and is considered a stronghold for these fish.

Deer Creek

Deer Creek

Deer Creek is an eastside tributary to the Sacramento River and second of the three Central Valley spring-run Chinook salmon strongholds in the Sacramento River watershed. It flows for approximately 60 miles from near the summit of Butt Mountain through meadows and dense forests before emerging on the Sacramento Valley floor. Deer Creek flows for 11 miles across the valley floor and enters the Sacramento River approximately 1 mile west of the town of Vina. Along with Central Valley spring-run Chinook salmon, Deer Creek also supports all life history stages of California Central Valley steelhead. The anadromous fish habitats in Deer Creek (along with Mill, Antelope, Battle, and Butte Creeks) are some of the best remaining habitats above the mainstem Sacramento River and serve as important anchors for their recovery.

Butte Creek

Butte Creek

Butte Creek originates on the western slope of the Sierra Nevada Mountains and enters the Sacramento Valley near the town of Chico. From there, it meanders southwesterly to the initial point of entry into the Sacramento River at Butte Slough. Butte Creek also enters the Sacramento River through the Sutter Bypass and Sacramento Slough. The Butte Creek watershed includes a series of dams, diversions, and canals, mostly located in lower Butte Creek. Butte Creek historically supported a self-sustaining population of Central Valley spring-run Chinook salmon and is currently one of three stronghold creeks for these fish in the Sacramento River watershed. Butte Creek is unique among the remaining Central Valley spring-run Chinook populations in that all holding and spawning areas are below 285 meters elevation. Since the 1990s, Butte Creek has undergone numerous successful restoration efforts as a result of collaborative partnerships with federal and state agencies and non-governmental organizations, such as the Friends of Butte Creek. Once impaired by dams with poor fish passage facilities and unscreened diversions, Butte Creek now provides fish ladders, fish screens, and dedicated instream flows for Central Valley spring-run Chinook salmon and California Central Valley steelhead trout.

Other watersheds within the Sacramento River Basin include: Antelope Creek, Big Chico Creek, Bear River (tributary to the Feather River), and Cow Creek.

Key counties with ESA-listed fish resources include:

  • Shasta
  • Tehama
  • Sacramento
  • Roseville
  • Placer

The Sacramento Basin Branch is also the lead for evaluating all Central Valley scientific research permits and programs including: hatchery management, flood management, California Department of Transportation and highway infrastructure projects, and Conservation Banking and In-Lieu Fee Programs (which extend beyond the Sacramento River Basin).

Endangered Species Act (ESA) Consultation and Involvement in Conservation Activities

  • Battle Creek winter-run Chinook salmon reintroduction implementation
  • Battle Creek and Clear Creek restoration programs
  • Butte Creek restoration and water resource management
  • Yuba River salmon recovery
  • Caltrans technical support
  • Central Valley hatchery management
  • Feather River and Oroville Dam operations
  • Fish screen consultations and fish passage improvement projects
  • Mitigation Banks, Conservation Banks, and In-Lieu Fee Programs
  • Safe Harbor and Habitat conservation planning and permitting
  • Salmon, steelhead, and sturgeon research and monitoring
  • Scientific research and enhancement of survival permitting
  • Species recovery planning and status reviews
  • State and Federal flood planning

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Last updated by West Coast Regional Office on August 28, 2020