The idea was straightforward. After World War II ended in 1945, the United States found itself with thousands of cargo ships, troop transports, and naval auxiliaries it no longer needed but might need again. Rather than scrap them, the Maritime Administration anchored them in protected waterways and placed them in preservation status -- engines cocooned in protective grease, hatches sealed, interiors dehumidified. The program began in 1946 under the United States Maritime Administration, known as MARAD. Suisun Bay offered ideal conditions: sheltered water, manageable currents, and proximity to the San Francisco shipbuilding infrastructure that could reactivate vessels quickly. During the Korean War and again during the Vietnam War, ships were pulled from the fleet, reactivated, and sent back to service. The mothball fleet was not a graveyard. It was a warehouse.

Decades of anchorage took their toll. The ships designed for 20-year service lives sat for 40, then 50 years. Paint systems formulated with lead, tributyltin, and other anti-fouling compounds began to fail. Flakes of toxic paint drifted into the bay with every tide. PCBs, heavy metals, and other hazardous materials leached from aging hulls into the estuary's sediment. Environmental groups and the State of California raised alarms. Congress funded the National Oceanic and Atmospheric Administration to study contamination in the fleet's vicinity, and NOAA's 2008-2009 sampling of sediment and bivalve tissue confirmed what advocates had feared: the ships were poisoning the bay. A lawsuit followed, brought by Arc Ecology, San Francisco BayKeeper, and the Natural Resources Defense Council against MARAD.

The settlement, reached in federal court in the Eastern District of California, imposed strict deadlines. Hazardous paint debris on vessel decks had to be removed within 120 days. All obsolete ships would be cleaned of flaking paint within two years. The 28 ships in worst condition were to be removed for disposal by September 2012, and the entire fleet of obsolete vessels by September 2017. Before removal, each ship would be sent to a local dry dock for cleaning -- scraping marine growth from underwater hulls, removing flaking paint above the waterline. Horizontal surfaces would be cleaned every 90 days, with monthly inspections and regular water sampling. No new ships with excess flaking paint would be admitted. MARAD began removing ships for recycling in November 2009, and the fleet shrank steadily through the 2010s.

The Suisun Bay anchorage has housed some remarkable vessels over the decades. The Glomar Explorer, built by Howard Hughes' companies as a cover for the CIA's secret recovery of a sunken Soviet submarine in 1974, spent years here after its covert career ended. The Sea Shadow, the Navy's experimental stealth ship that tested radar-invisible hull designs in nighttime runs across the bay, was stored here before being scrapped in 2012. The USS Iowa, a World War II battleship that saw action from the Marshall Islands to Okinawa and returned to service during the Korean War, anchored here before being moved to the Port of Los Angeles as a museum ship. Each vessel carried decades of classified history in its hull, waiting quietly alongside rusting Liberty ships and forgotten cargo carriers.

In January 2016, the Department of Transportation and MARAD announced that the Suisun Bay site would close by February 2017, leaving only the James River Reserve Fleet in Virginia and the Beaumont Reserve Fleet in Texas as active reserve anchorages. That closure never quite happened. As of 2025, the Suisun Bay Reserve Fleet remains occupied, though its population has dwindled to single digits. The remaining ships sit in water depths ranging from 8 to 14 meters at low tide, within a regulated navigation area running northeast from the Union Pacific Railroad Bridge, parallel to the Benicia shoreline. The fleet that once represented American industrial might and military preparedness now represents something else entirely: the difficulty of cleaning up after a century of strategic ambition.