The Mokelumne River Hatchery was built in 1963 to offset the loss of fish spawning habitat due to the construction of Camanche Dam by East Bay Municipal Utility District (EBMUD).
From 1987 to 1992, there was a drought in the area. Low flows and a series of fish kills reduced the Mokelumne River steelhead run during the 1980s.
In response, EBMUD implemented several programs to improve water quality, flow regimes, and physical habitat in the lower Mokelumne River. The hatchery was remodeled in July 2002, enlarging the rearing space to promote fish health and fish survival rates while also making hatchery operations more efficient.
Since then, the Lower Mokelumme River Fishery Resource has thrived, as evidenced by counts of fall-run Chinook salmon escapement or returning salmon. Returning salmon increased by 3,028 from 1998 to 2003.