In 1972, the U.S. Army Corps of Engineers recommended establishing a national wildlife refuge in the Stone Lakes Basin after completing a flood control study of Morrison Creek, Sacramento County's largest creek system. In 1994 following six years of study and public meetings, the U.S. Fish & Wildlife Service (Service) established Stone Lakes NWR in Elk Grove, Sacramento County, California. It is the 505th refuge in the NWR System and one of the few urban refuges in the nation.

Located in southern Sacramento County about ten miles south of the state capital, the refuge project area encompasses 18,200 acres - the area roughly bounded by the town of Freeport, Interstate 5, the town of Walnut Grove and the Sacramento River.

With its rich mosaic of Central Valley native habitats - grassland, permanent and seasonal wetland, vernal pool, riparian and oak forest - the Stone Lakes basin supports a diversity of native wildlife and plant species. The Refuge's prime location on the Pacific Flyway attracts the full range of migratory birds.