San Francisco Naval Shipyard The San Francisco Naval Shipyard was a United States Navy shipyard in San Francisco , California , located on of waterfront at Hunters Point in the southeast corner of the city . Originally , Hunters Point was a commercial shipyard established in 1870 , consisting of two graving dock s purchased and upbuilt in the late nineteenth and early twentieth century by the Union Iron Works company , later owned by the Bethlehem Shipbuilding Company and named Hunters Point Drydocks , located at Potrero Point . History . The original docks were built on solid rock . In 1916 the drydocks were thought to be the largest in the world . At over 1000 feet in length , they were said to be big enough to accommodate the world ' s largest warships and passenger steamers . Soundings showed an offshore depth of sixty - five feet . During the early 20th century much of the Hunters Point shoreline was extended by landfill extensions into the San Francisco Bay . Between World War I and the beginning of World War II the Navy contracted from the private owners for the use of the docks . The docks provided deep - water facilities between San Diego and Bremerton , Washington . The main naval base in the area was at Mare Island Naval Shipyard , but the continuous silting in the area made it only suitable for relatively shallow - draft ships . A Congressional hearing on Pacific Coast Naval Bases was held in San Francisco in 1920 at San Francisco City Hall , wherein city representatives , Mayor Rolph , City Engineer O ' Shaughnessy and others testified on behalf of permanently siting the Navy at Hunters Point . At the start of World War II the Navy recognized the need for greatly increased naval shipbuilding and repair facilities in the San Francisco bay area , and in 1940 acquired the property from the private owners , naming it Hunters Point Naval Shipyard . The property became one of the major shipyards of the west coast . It was later renamed Treasure Island Naval Station Hunters Point Annex . During the 1940s , many workers moved into the area to work at this shipyard and other wartime related industries . The key fissile components of the first atomic bomb were loaded onto the USS Indianapolis in July 1945 at Hunters Point for transfer to Tinian . After World War II and until 1969 , the Hunters Point shipyard was the site of the Naval Radiological Defense Laboratory , the US military ' s largest facility for applied nuclear research . The yard was also used after the war when ships from Operation Crossroads were decontaminated . Because of all the testing , there is widespread radiological contamination of the site . After the war , with an influx of blue collar industry , the area remained a naval base and commercial shipyard . The Navy operated the yard until 1974 , when it leased most of it to a commercial ship repair company . The Navy closed the shipyard and Naval base in 1994 as part of the Base Realignment and Closure Commission ( BRAC ) . In addition to radioactive contamination , Hunter ' s Point had a succession of coal - and oil - fired power generation facilities which left a legacy of pollution , both from smokestack effluvium and leftover byproducts that were dumped in the vicinity . The BRAC program manages the majority of the site to this day , and is engaged in various pollution remediation projects .