Historically winter Chinook salmon spawned in the upper reaches of tributaries to the Sacramento River including the McCloud, Pit and Upper Sacramento Rivers. Upon completion of Shasta (1945) and Keswick (1950) Dams access to this historic spawning habitat was blocked. With the completion of these dams the spawning area for winter Chinook salmon was reduced to the area just downstream of Keswick Dam. Populations of winter Chinook salmon declined over the years, and in 1989 the winter Chinook salmon were listed as endangered under the California Endangered Species Act and as threatened under the Federal Endangered Species Act. In 1993 the population of returning adults reached an all time low of 186 individual fish, and in 1994 the population was relisted as endangered under the Federal Endangered Species Act.
In 1997 the hatchery was established and in April 1998 the hatchery released their first winter Chinook salmon, and has been in continuous operation since.