During World War II, dewatering of the Penn mine resulted in fish kills that essentially wiped out the salmon in the Mokelumne. As a result, EBMUD was required to maintain a fish hatchery at the dam, but, because there was no requirement that the utility maintain adequate river flows necessary for the fish to survive once they left the hatchery, the kills recurred.
In 1977, major fish kills because of mine wastes in the Camanche reservoir resulted in the issuance of a Cleanup and Abatement Order to New Penn Mines, the owner of the mine. The order was ignored, as were most subsequent orders.
Other attempts to deal with New Penn Mines also failed, and in March 1979, EBMUD, the state Department of Fish and Game (DF&G), and the Central Valley Regional Water Quality Control Board agreed to a joint cleanup of the mine discharges. They built surface diversion ditches and a series of ponds along Mine Run creek above the point where it drains into the river.