The accord between the state Department of Parks and Recreation and Deltakeeper results from a federal lawsuit filed by the environmental organization in 2004.
The suit charged that storm runoff from a former gold mine at Empire Mine State Park in Grass Valley is polluting Little Wolf Creek which flows into the Sacramento River.
Under terms of the agreement, the state and representatives of Deltakeeper will work together to stem the flow of toxic runoff from the mine.
Carrie McNeil, a spokeswoman for Deltakeeper says the cleanup will take awhile.
"One of the major issues with mine tailings is actually the fish contamination with mercury tissue throughout the entire bay-delta area. Progress will take a long time to clean up the levels of mercury and the fish."
Empire Mines produced tons of gold as well as toxic waste for over a century. Nearly 50-thousand tons of toxic sediment was removed from a mine as part of a three-year cleanup that concluded in 1989.