The board said pollutants shed by the ships into Suisun Bay include mercury, lead, hexavalent chromium, PCBs and asbestos.
The federal government's maintenance of the mothball fleet anchored off Benicia violates clean water and hazardous waste laws, a judge said Thursday.
More than 20 tons of paint containing lead has flaked off into the water where fish and birds live.
The ruling is not only good news for the wildlife, it's a victory for environmentalists who have sued to get the ships cleaned up.
"The federal government has been operating an illegal hazardous waste facility in San Francisco Bay for years," Michael Wall, a lawyer for the Natural Resources Defense Council told the Contra Costa Times. "It's clear it has to clean this site up."
Wall said environmental groups plan to push for a speedy and clear cleanup plan during a trial in June.