Historical Fish Community and Efforts to Restore Native Fish to the San Joaquin River, California

Fish communities in the San Joaquin River basin have changed markedly in the last 150 years. Before Euro-American settlement, the river supported a distinctive native fish fauna that had evolved over a period of several million years. These native fish assemblages were adapted to widely fluctuating riverine conditions, ranging from large winter and spring floods to warm low summer flows. These environmental conditions resulted in a broad diversity of fish species that included cold-water anadromous salmonids as well as cold and warm-water resident fish species.

As the land and water resources of the San Joaquin Valley were developed, riverine habitat conditions for native fish species deteriorated. The loss of habitat, combined with the introduction of non-native fish species, precipitated a decline in both abundance and distribution of native species and unique assemblages of these species. Current habitat conditions bear little resemblance to those under which native fish communities evolved, reflecting the effects of significant human disturbance.

Fish assemblages currently found in the San Joaquin River are the result of substantial changes to their physical environment, combined with more than a century of non-native fish and exotic invertebrate introductions. Areas where unique and highly endemic fish assemblages once occurred are now inhabited by assemblages composed primarily of introduced species. Factors likely influencing native fish species abundance and distribution include dewatered stream reaches, altered flow regimes and reductions in flow, reductions in the frequency, magnitude, and duration of floodplain inundation, isolation of floodplains from the river channel by channelization and levee construction, changes to sediment supply and transport, habitat fragmentation by physical barriers, creation of false migration pathways by flow diversions, and poor water quality. Despite these conditions, many native fish species still persist in the basin, underscoring the potential for enhancing native aquatic communities in the San Joaquin River.

The San Joaquin River Restoration Program’s Restoration Goal is "to restore and maintain fish populations in ‘good condition’ in the mainstem San Joaquin River below Friant Dam to the confluence with the Merced River, including naturally reproducing and self-sustaining populations of salmon and other fish". Although the focus of the restoration program is on spring-run Chinook salmon, restoration actions implemented for salmon are expected to improve conditions for many other native species. We will discuss the proposed approach to restoring and maintaining populations of "other fish" in good condition.