BENICIA — The last of 57 decaying ships in the federal government’s iconic mothball fleet has left Suisun Bay, ending a long struggle over toxic ship pollution into waters by a major fish nursery area and migration route.

The cargo ship Cape Borda is heading to a Texas dismantling yard — a trip that was scheduled to begin Friday morning but postponed due to tugboat problems, the US Maritime Administration reported .

The Borda is the last of 57 military reserve or “ghost” ships required to leave Suisun Bay under a legal settlement between the federal Maritime Administration and state environmental regulators and groups.

Created after World War II to store warships and cargo ships in case needed for a national emergency, the fleet’s hulking gray figures created an indelible landmark that motorists saw as they zipped over the Interstate 680 Benicia/Martinez bridge between Contra Costa and Solano counties.

But toxic paint, PCBs and heavy metals from the mothballed ships polluted Suisun Bay along California’s biggest migratory route for salmon, steelhead trout, striped bass and other fish that migrate from the sea up rivers to spawn.

“The removal of the Cape Borda brings to an end an ongoing source of pollution that threatened the bay and the rich aquatic life it supports for decades,” said David Elias, a senior engineering geologist with the San Francisco Regional Water Quality Control Board, a state water pollution agency. “We thank everyone involved in identifying this environmental threat, and working with us to get it corrected.”

A ceremony to mark the event was held Thursday at the Mare Island Dry Dock, where the Cape Borda was scrubbed clean of invasive species to prepare it for its final trip to the scrap yard..

“Here is perhaps no greater symbol of the maritime industry’s environmental progress than what has been accomplished here,” said Joel Szabat, the Maritime Administration’s administration director.

While fewer than 10 reserve ships are still anchored in the reserve fleet east of the Interstate 680 Benicia/Martinez bridge, these ships are maintained, cleaned and kept ready to be called into service — unlike the 57 obsolete ships.

“The 57 ships become abandoned toxic junk,” said Sejal Choksi-Chugh, executive director of the Oakland-based San Francisco Baykeeper, an environmental watchdog group. “Their removal is a milestone in cleaning and protecting the bay.”

The Maritime Administration initially resisted requests to stop the pollution, but the agency did a very good job of cleaning and removing them once the court agreement was made, both Choksi-Chugh and Elias said.

Among the remaining ships are two World War II U.S Coast Guard bayou tenders and several fleet and logistic support ships, according to federal records.

With the Cape Borda’s departure, the Maritime Administration beats its Sept. 10 deadline, as required under the legal settlement, to remove the last “Ghost Fleet” ship from Suisun Bay. The lawsuit was filed in 2009 by the Natural Resources Defense Council, San Francisco Baykeeper and Arc Ecology. The regional water board intervened in the suit, which led to the 2010 agreement to remove the ships.

Launched in 1967, the Cape Borda was once part of the National Defense Reserve Fleet, which provided a reserve of ships for national defense and emergencies. The Cape Borda hauled bulk cargo between the Gulf of Mexico for 18 years before the Maritime Administration acquired it and based it in Alameda. The ship was later activated to support the Desert Storm campaign in 1990.

Staff writer Thomas Peele contributed to this story.