Suisun Bay Reserve Fleet The Suisun Bay Reserve Fleet is located on the northwest side of Suisun Bay ( the northern portion of the greater San Francisco Bay estuary ) . The fleet is within a regulated navigation area that is about 4 1 / 2 miles long and 1 / 2 mile wide . It begins just north of the Union Pacific Railroad Bridge and runs northeast , parallel to the shoreline { maps . google . com LINK } . Water depths range from about 14 meters ( 45 feet ) at Mean Lower Low Water ( MLLW ) at the foot of the anchorage , to about 8 meters ( 26 feet ) MLLW at the shallowest berths towards the northern end of the anchorage . Purpose . The U . S . Maritime Administration ( MARAD ) maintains the National Defense Reserve Fleet , a fleet of vessels that serve as a reserve of ships for national defense and national emergency purposes . The reserve fleet program was begun in 1946 at the end of World War II . At its peak in 1950 , the program had more than 2 , 000 ships in lay - up . One of the reserve fleet storage sites is in Suisun Bay , the northern portion of San Francisco Bay . Only 55 vessels currently remain with the Suisun Bay Reserve Fleet . Environmental issues . The State of California and several environmental groups have raised concerns about the environmental impacts of the fleet . Potential concerns include heavy metals and anti - fouling agents in the paint that is peeling off of the vessels , as well as PCBs and other hazardous materials that may have been released . Congress responded to these concerns by funding the National Oceanic and Atmospheric Administration ( NOAA ) to design and implement a study of contaminants in the vicinity of the fleet . NOAA ' s DARRP program began work on this project in January 2008 . Since then , NOAA ' s team has assessed existing data from the area to determine data gaps , researched the history and environmental setting of the site , discussed the project with numerous stakeholders , conducted a site visit , and developed and refined and sampling and analysis plan . NOAA deployed bivalve samples in June 2008 and collected sediment and bivalve tissue samples from the area in July 2008 . A second field sampling event for additional tissue samples occurred in September . These samples were analyzed and a data report was delivered in early 2009 . Based on these findings , the United States Government has reached an agreement with Arc Ecology , San Francisco BayKeeper , Natural Resources Defense Council , and the California Regional Water Quality Control Board , San Francisco Bay Region ( Regional Board ) regarding the maintenance and disposal of obsolete ships owned by the U . S . Department of Transportation ’ s Maritime Administration ( MARAD ) at the Suisun Bay Reserve Fleet site , resolving a lawsuit in the Eastern District of California . Under the agreement , MARAD will clean , maintain , and dispose of these ships in a manner that eliminates sources of Bay pollution . The Maritime Administration has already begun removing obsolete ships from Suisun Bay for recycling — several ships have left since November 2009 . A total of 11 ships remain . Under the terms of the settlement : Current inventory . As of June 15 , 2013