Bay Area Military Bases
Historical Essay
by David D. Schmidt, 2026
An excerpt from the book, San Francisco Bay Area: An Environmental History, by David D. Schmidt (Backcountry Press, 2025).
This is a survey of former and current military bases around the San Francisco Bay, but is not a full list of all such sites.
Presidio's Crissy Field, December 1955.
Photo: OpenSFHistory.org wnp25.7013
Presidio of San Francisco
As a U.S. Army base from 1846 until 1994, the two-square-mile Presidio had a tidal lagoon that was partially filled with trash in the late 1880s to 1912. By 1913, the remaining tidelands were filled with dredged mud from the bay, and converted to a military airfield, Crissy Field, in 1919-1921. The Army later paved 70 acres of Crissy Field for an asphalt runway. The airfield closed in 1974, but the asphalt remained.
Before turning the Presidio over to the National Park Service in 1994, the Army mapped dozens of dump sites and areas with soil or groundwater contaminated by fuel leaks or hazardous waste. The base had been dumping all its waste within the Presidio until the 1970s. Cleanup efforts funded by the Army were underway throughout the 1990s and early 2000s, and completed by 2014.
The historic Crissy Field trash dump was carefully exhumed by archeologists in 1999, who turned up over 80,000 artifacts. To restore the lagoon, workers removed 230,000 cubic yards of material, including 15,000 tons of rubble from the 1906 Earthquake, and 87,000 tons of hazardous waste, mostly soil contaminated by leaking fuel storage tanks. By 2003, Crissy Field was one of San Francisco's most popular parks.
Benicia Barracks in the backgroound as well as a closer view of some of Benicia Arsenal buildings.
Photo: National Archives Old Army and Navy Record Group. Courtesy of the Benicia Historical Museum, Benicia, California.
Benicia Arsenal, Solano County
The Benicia Arsenal, established in 1851, grew to about five square miles during World War II, when it stored bombs, artillery shells and chemical weapons. In the late 1950s, the Army surveyed the sprawling site and found live bombs and ammunition scattered in open fields. After removing the unexploded ordnance, the Army closed the base in 1962 and turned most of the land over to the city of Benicia. City officials, desperate to bring in new industry, were happy to get Exxon to build an oil refinery (in 1966) on the former base. Over the next 40 years, housing developments went up along the arsenal’s perimeter, and children played in fields with bombs just below the ground. One developer called the Concord Naval Weapons Station four times to remove or blow up bombs and ammunition found during excavations for new homes.
In 1996, Benicia residents walking near their homes discovered abandoned ammunition and signal flares. The state Department of Toxic Substances Control (DTSC) ordered developer Granite Management to stop building and search the property with metal detectors. The search turned up six pieces of unexploded ordnance.
Camel barns at the Benicia Arsenal, photographed in September 1967 by Aero Photographers of Sausalito, California. In the 1850s the U.S. Government brought dromedaries to the West for experimentation in logistics. Lieutenant Edward F. Beale, USN, used them in survey work. In November 1863 thirty-four of the animals were moved from southern California to the Naval Arsenal at Benicia, where they were sold at auction on 26 February 1864. This photograph shows the buildings in which they were kept.
Mare Island Naval Shipyard
Mare Island, the Bay Area’s first naval base, employed 35,000 people during World War II, building more than 400 ships. In the 1960s to 1990s, the shipyard serviced nuclear submarines. By the time the base closed in 1996, portions of its soil and groundwater were contaminated by hazardous wastes. One 70-acre parcel included a former trash landfill, an oil disposal yard, a lead-acid battery disposal area, and an industrial wastewater treatment plant. By 2005, with cleanup still underway, redevelopment had begun in clean areas, with the first new homes.
Mare Island drydock, 2024.
Photo: Chris Carlsson
Aerial view of Moffet Field looking northeast.
Photo: nara.getarchive.net
Moffet Naval Air Station, Sunnyvale
Moffett Field, established in 1933, was built on former farm fields and bayside marshes. The base had three on-site waste dumps. The first, used from 1933 to the late 1940s, is visible today as a low mound on a nearby golf course.
The second, a five-acre landfill east of the main runway, received waste from the late 1940s to 1963. The third, a 22-acre landfill, north of the runway, accepted waste from 1963 through the mid-1970s. These two landfills were suspected of contaminating shallow groundwater with fuel, solvents, and PCBs. This groundwater was naturally salty and undrinkable, but in 1997, to prevent the spread of contaminated groundwater into the bay, contents of the second landfill were moved to the third and capped with layers of heavy plastic, clay, and soil. This landfill contains 423,000 cubic yards of waste.
In the 1990s, the Navy turned over the 3-square-mile facility to NASA, which runs the adjacent Ames Research Center. But the Navy continued cleaning up groundwater contaminated by leaking fuel storage tanks, and soil contaminated with toxic DDT, PCBs, and hydrocarbons.
Alameda Naval Air Station
In 1936, President Franklin Roosevelt bought 4.4 square miles of land for a Naval Air Station from the City of Alameda for the token sum of $1. At the time, most of this "land" was actually shallow bay waters and wetlands, filled by the Navy with sand and mud dredged from the bay over the next five years. The base was commissioned in 1940, and closed in 1996. By this time, it had 24 sites contaminated with metals, pesticides, fuels, and other toxics, including two 110-acre landfills. One site contained oily wastes dating back to the late 1800s from the Bay Area's first oil refinery. Cleanup work, funded by the Navy, continued for decades.
Alameda Naval Air Station, early 2000s.
Photo: Center for Land-Use Interpretation
Hunters Point Naval Shipyard
Located on a narrow peninsula at the southeast corner of San Francisco, the shipyard began as a private drydock in 1869. During World War I, Bethlehem Steel built ships there. The Navy bought the drydock and much of the peninsula in 1941, and during World War II quickly expanded the ship repair facility, bulldozing the hilly peninsula to add hundreds of acres of bay fill soon covered by streets, machine shops, and warehouses.
During the war, Hunters Point was one of the nation's biggest military ports. In 1946, the Navy established the Naval Radiological Defense Laboratory (NRDL) here, employing up to 600 people until its closure in 1969. In the late 1940s, the Navy sent 14 surplus ships contaminated with radiation from nuclear bomb tests to Hunters Point, where NRDL experimented with decontamination methods, such as sandblasting and acid. The lab also performed radiation experiments on thousands of live animals, including dogs, pigs, rats and mice.
Some of the lab’s waste was dumped on the base, and some was stuffed into 55-gallon drums and dumped at sea near the Farallon Islands, including the irradiated animal carcasses. In one case, 125 tons of radioactive sandblast waste was sold to a construction contractor. In the 1960s, the shipyard had a 46-acre landfill that was receiving 40 tons of waste per day, including hazardous waste.
Hunter's Point Naval Shipyards, 1957, jammed with ships.
Photo: Prelinger Archives
After the base closed in 1974, the Navy leased part of it to Triple A Machine Shops Inc., from 1976 until 1986. Triple A allegedly dumped toxic heavy metals and PCBs in the landfill. Groundwater was found to be contaminated with dissolved metals, petroleum byproducts, and other chemicals. In 1996 San Francisco District Attorney Terence Hallinan recovered $1.1 million in cleanup costs from Triple A.
In 2000, a federal judge ordered another shipyard tenant, Astoria Metals Corp., to stop dumping contaminated water in the bay. In August 2000 the landfill, though covered with soil, caught fire and smoldered for a month before the Navy extinguished it.
U.S. EPA added the base to its Superfund National Priorities List in 1989, but the Navy remained responsible for cleanup, spending $1.2 billion by 2024. In 2005, the Navy turned over a clean portion of the base to San Francisco for redevelopment. In 2018, two employees of a cleanup contractor hired by the Navy, Tetra Tech EC, were found to have falsified lab tests of soil samples. The Navy re-tested 1/3 of the areas originally tested by the contractor. By 2024, developer Lennar had built 582 condominiums in the clean area, known as Shipyard.
Hamilton Air Base main gate, 1950s.
Photo: Hamilton Base Museum
Hamilton Field
Located on the San Pablo Bay shoreline north of San Rafael, Hamilton Field was dedicated as an Army air base in 1934, transforming a square mile of diked farmland known earlier as Marin Meadows. The Air Force closed it in 1974. For the next 20 years, its future was the subject of heated debate in Marin County. Hundreds of homes were built starting in the late 1990s, but some of them were plagued by gases migrating underground from the base's 15-acre trash landfill.
The waste had high levels of toxic chemicals, including lead and other heavy metals, pesticides such as DDT, and fuel. To keep these toxics from migrating with rainfall percolating through the landfill, the Air Force installed a high-strength plastic cap on the landfill site in 1995.
In 2001, methane gas from the landfill had seeped underground to within 100 feet of a tract of new homes. If the gas got into a home, any spark could cause an explosion. Construction halted while the Air Force, under orders from the Regional Water Quality Control Board, installed a subterranean wall around the landfill, to keep the methane away from any buildings.
Concord Naval Weapons Station
The Concord Naval Weapons Station, a 20-square mile military arsenal, began operation at Port Chicago in late 1942, when the Navy invoked eminent domain to buy out the entire port town on Carquinez Strait and evict its 3,000 residents. During World War II, the port shipped about 100,000 tons of ammunition.
On July 17, 1944, in the war’s deadliest home-front disaster, two ships and a train filled with bombs and munitions exploded, killing 320 servicemen and injuring 390. The blast shattered windows 40 miles away at San Francisco’s St. Francis Hotel. Nearly all the men killed were African-American sailors.
Black sailors handling live ammunition at Port Chicago, 1943.
Photo: Wikimedia
Between 1942 and 1979, the Navy buried over 33,650 tons of trash, solvents, paints, and munitions in landfills on the base. The Navy's cleanup began in 1980, with the goal of preventing toxics from polluting groundwater outside the base. The U.S. EPA placed the base on its Superfund National Priorities List of toxic sites in 1994.
The base included salt marsh habitat for the endangered California clapper rail, and inland grasslands that supported about 600 cattle and a herd of 55 tule elk, introduced in 1976 by the state Department of Fish and Wildlife. In 1984, more than four square miles of wetlands adjoining Carquinez Strait were set aside as a wildlife refuge. The tule elk were removed in 2006.
In 1999 the port area, about 12 square miles, was leased to the U.S. Army and renamed Military Ocean Terminal Concord, while the Navy closed the 8-square-mile inland portion of the base. In 2019 the Navy transferred four square miles of rolling hills to the East Bay Regional Park District; in 2023 the city of Concord moved ahead with plans to redevelop the other four square miles with 13,000 new homes.
2006 aerial shot of Concord Naval Weapons depot.
Photo: Wikimedia
Point Molate
Point Molate, a hilly ridge on the East Bay shoreline between the Richmond-San Rafael Bridge and the Chevron Oil Refinery, is the site of a 290-acre Navy fuel depot with 24 buried concrete tanks that held more than 50 million gallons of fuel for the Navy's Pacific Fleet from World War II until it closed in 1995. The location was strategic: far enough inside the Golden Gate to be safe from naval attack, and adjacent to the Bay Area's largest oil refinery (Chevron).
Cleanup of soil contaminated by leaks from the fuel tanks began in 1988 and took more than 20 years. In 2024, environmental groups were fighting the City of Richmond’s plan to redevelop the scenic shoreline with luxury homes, and instead make it a regional park.
Point Molate.
Photo: Jack Scheinmore
Travis Air Force Base
Established in 1943, the nine-square-mile Travis Air Force Base, near Fairfield in Solano County, was still in use in 2024. From the 1940s through the 1970s, Travis had several toxic spill and disposal sites. Three landfills on the base accepted wastes from 1943 to 1977; one was a known source of water pollution by 1970. A jet fuel spill in 1978 killed all aquatic wildlife along two miles of Union Creek. A storm sewer system was found to contain chemical wastes flushed down drains from base workshops.
The U.S. EPA put the base on its Superfund National Priorities List for cleanup in 1989, and the Air Force began cleanup work in 1997.
Travis Air Force Base, c. 2010s.
Photo: Heidi Couch, dvidshub.net
The Lawrence Livermore National Laboratory and Nuclear Sites
In 2001, the U. S. Department of Energy (DOE) published a national directory of sites used for nuclear weapons and radiation work in the 1940s through the 1990s, where people may have been exposed to radiation. Bay Area sites included Dow Chemical Co. in Walnut Creek, General Electric's Vallecitos nuclear facilities (see Electric Power Chapter), Stanford’s Linear Accelerator Center in Palo Alto, the Lawrence Berkeley Lab and the Lawrence Livermore National Lab (LBL and LLNL, both run by UC Berkeley). The most serious health threats were found at the Livermore Lab, which is on EPA's Superfund National Priorities List.
The LLNL’s primary function has been nuclear weapons research. It was first used as a Naval Air Station during World War II, then transferred to the U.S. Atomic Energy Commission (now part of DOE) in 1951.
From the 1940s to the 1980s, the LLNL created, used and dumped a variety of hazardous materials, including radioactive wastes. In 1984, the California Department of Health services (CDHS) ordered LLNL to provide alternate water supplies to residents west of the facility, whose drinking water wells had been contaminated by carcinogenic chemicals.
Within the site, fuels and radioactive tritium were found in groundwater. Cleanup operations removed soil contaminated with solvents, radioactive wastes, heavy metals, PCBs, and fuel. By 1997, LLNL had built five groundwater treatment plants, pumping contaminated water from beneath the site, vaporizing the contaminants, and pumping clean water back into the ground. This was expected to continue through at least 2030.
Aerial view of Lawrence Livermore National Laboratory, 2011.
Photo: U.S. Department of Energy
Questions? Email the author: davidnaturesf@gmail.com
Excerpted from David D. Schmidt's San Francisco Bay Area: An Environmental History. Available from Backcountry Press.