Though the NRDL was shut down in 1969,  Hunters Point remained active until 1974, when it was decommissioned and placed on industrial reserve. In 1976, the majority of the land was leased to Triple A Machine Shop, Inc. who used it for ship repair.

On October 5, 1994, the US Navy was sued by a coalition of environmentalist, sports fishing, and public interest groups who alleged that toxic discharges from Hunters Point Naval Shipyard were contaminating San Francisco Bay. Though the alleged violations reached 19,000, the extent of the toxic mess buried on the south side of the base remains a mystery, largely due to the NRDL's shipshod documentation during their top secret research.