Sacramento - San Joaquin




Text modified from Abell et al. 2000. Freshwater Ecoregions of North America: A Conservation Assessment. Island Press, Washington, DC, USA. Additional text provided by Jennifer Hales.


United States

Major Habitat Type

Temperate coastal rivers

Drainages flowing into

The Sacramento and San Joaquin rivers join in the Central Valley to form an inland delta, which then drains the Suisun, San Pablo and San Francisco bays to the Pacific Ocean (Minckley et al. 1986).

Main rivers to other water bodies

Within the ecoregion, the main freshwater systems are the Sacramento-San Joaquin rivers, the Pit River, ClearLake, the Pajaro-Salinas system, and the upper Kern River.



This ecoregion lies almost entirely within the state of California, encircling the Central Valley and including the western drainages of the Sierra Nevada mountains. A tiny portion also lies just inside the northeast corner of Nevada.


The Central Valley is a large, flat valley that is bordered by the Sierra Nevada to the east and the Coast Ranges to the west.

Freshwater habitats

The confluence of the Sacramento and San Joaquin rivers form an inverted river delta that flows into San Francisco Bay, the largest estuary on the West Coast of North America. This area once supported enormous populations of migratory waterfowl in extensive freshwater marshes (Ricketts et al. 1999). Riparian woodlands were also once more extensive, and bordered many of the valley’s major rivers and tributaries. Vernal pool communities occur within the Central Valley in seasonally flooded depressions, including those that are saline or alkaline, terrace pools, and pools on volcanic soils. Several aquatic invertebrates are restricted to these habitats (Ricketts et al. 1999).

Terrestrial habitats

In addition to the high diversity of freshwater habitats, this ecoregion also once supported one of the most diverse, productive, and distinctive grasslands in temperate North America, including prairies, oak-grass savannas, and desert grasslands (Ricketts et al. 1999).

Description of endemic fishes

Of the fish species endemic to the ecoregion,  many have localized distributions. Species with historically small ranges include the extinct Clear Lake splittail (Pogonichthys ciscoides), and the rough sculpin (Cottus asperrimus). The primitive Sacramento perch was once widespread throughout the Sacramento-San Joaquin system, but today inhabits a much reduced range due to its inability to compete with introduced centrarchids (Moyle 1976). Other endemics include the hardhead (Mylopharodon conocephalus), Sacramento pikeminno (Ptychocheilus grandis), and splittail (Pogonichthys macrolepidotus).

Ecological phenomena

The ecoregion is considered biologically outstanding because it contains the southernmost populations of five anadromous fish as well as four runs of Chinook (Abell et al. 2000).

Justification for delineation

Ecoregion boundaries are taken from Abell et al. (2000) and are based on subregions defined by Maxwell et al. (1995). Modifications to the boundaries of this ecoregion were based on a biogeographic assessment performed by The Nature Conservancy. The boundaries were modified to exclude the Surprise Valley watershed, now placed in the Oregon Lakes [124] ecoregion.


  • Abell, R.,Olson, D.,Dinerstein, E.,Hurley, P. T.,Diggs, J. T.,Eichbaum, W.,Walters, S.,Wettengel, W.,Allnutt, T.,Loucks, C. J.;Hedao, P. (2000). "Freshwater ecoregions of North America" Washington, D.C.: Island Press.
  • Moyle, P. B. (1976). "Inland fishes of California" Berkeley: University of California Press.
  • Ricketts, T. H.,E. Dinerstein,D.M Olson;C.J. Loucks (1999). "Terrestrial ecoregions of North America: A conservation assessment" Washington, D.C.: World Wildlife Fund.
  • Maxwell, J. R., Edwards, C. J., Jensen, M. E., et al. (1995) \A hierarchical framework of aquatic ecological units in North America (Nearctic Zone)\ St. Paul, MN. North Central Forest Experiment Station, USDA Forest Service.
  • Minckley, W. L., D. A. Hendrickson, and C. E. Bond (1986). "Geography of western North America fishes: description and relationships to intracontinental tectonism" C. H. a. E. O. W. Hocutt (Ed.) The zoogeography of North American freshwater fishes New York: John Wiley & Sons.