Historically, the river had strong runs of anadromous native spring and fall Chinook, Coho, steelhead, sea-run cutthroat, and pacific lamprey. There is also a remnant population of ESA listed bull trout. Currently, summer steelhead and both Chinook runs are listed with very high extinction risks.
Various factors that limit these populations include stray hatchery fish interbreeding with wild fish and degradation of tributary habitat. Irrigation withdrawals and impaired habitat diversity and complexity are results of various land use practices in the watershed. Fish passage at a larger dam, Powerdale, will be alleviated soon, as its removal is expected to be completed by November 2010. Other threats include fine sediment from rural roads, competition from hatchery fish, elevated water temperatures due to land use, toxins from agricultural practices, altered hydrology due to low-head hydro diversions and upslope land use.