Gravel extraction along the south bank of Alameda Creek dates to at least 1912, when the Niles Sand and Gravel Company began processing river-bed material for concrete production. In 1954, the company expanded into the area that now forms the park. By 1969, some pits had been excavated to 120 feet below the surface, well below the water table. The Alameda County Water District had been purchasing water for groundwater recharge of the Niles Cone aquifer, and that water kept flooding the quarry pits. The company's solution was brute force: pump the water out. When the company sued the water district in 1972, arguing that the recharge program damaged its operations, the court found that the pits would have flooded naturally regardless and ruled the pumping illegal.

Between 1975 and 1992, the East Bay Regional Park District and the Alameda County Water District purchased the land that would become Quarry Lakes. Conversion to parkland began in 1997, with the water district continuing restoration projects beyond 2017. The park sits between the old communities of Centerville and Niles in Fremont, bounded to the northeast by BART tracks and to the south and west by Alameda Creek. The transformation was not cosmetic. It involved reshaping shorelines, establishing native plant communities, and creating conditions for wildlife to return to a landscape that had been stripped to bedrock.

The lakes at Quarry Lakes are arranged in an ecological hierarchy. Because they play a critical role in groundwater percolation, only two of the larger lakes are open to public water contact. Horseshoe Lake is stocked regularly with rainbow trout and channel catfish and includes a swimming complex and a boat pier, though gasoline motors are prohibited to prevent water contamination. Rainbow Lake hosts resident populations of largemouth bass and smallmouth bass. Lago Los Osos and Willow Slough are open for nature observation only, and two additional unnamed lakes are closed entirely for the water district's use. At the south end of the park, a grove of bald cypress rises unexpectedly from the California landscape, while a rare fruit grove on the Horseshoe Lake peninsula mixes native and exotic trees.

As one of the few riparian zones in near-natural condition along Alameda Creek, Quarry Lakes has become an important stop on the Pacific Flyway. Restoration projects have attracted wood ducks, great blue herons, and snowy egrets. Nesting boxes and strategic berry plantings have drawn smaller species like tree swallows, northern flickers, and salt marsh yellowthroats. The irony is rich: a landscape destroyed by industrial extraction has become, through deliberate restoration, a more ecologically diverse habitat than the farmland that surrounded it before the quarry arrived. In 2010, a demonstration garden of native and drought-resistant plants was established along Horseshoe Lake through a University of California extension program.