State biologists say beneath the surface of the water, pollution problems have been brewing for decades with a buildup of copper, DDT and PCBs.
"Small organisms are exposed to them and then as the larger fish feed on the smaller fish, those pollutants become highly magnified," said Samuel Unger is with the California Regional Water Quality Control Board.
Unger says the state is looking at a handful of plans to clean up the marina, some of which would remove pollution by dredging the entire harbor and restricting boat paints that contain copper biocides -- the chemical that keeps algae and barnacles from coating the hulls of these boats.
"The boats are leaching copper into the waters of Marina del Rey," said Unger.
The concern here at the marina, though, is the price tag associated with these cleanup plans. Opponents say many boat owners may just leave when faced with the cost of repainting their boats.
"If we have to strip every boat here and put non-toxic bottom paint on the bottom, using the water board's own estimate, at $8,000 a boat times 5,000 boats, that's $40 million," said Greg Schem, owner of the Boatyard, a marine maintenance company in Marina del Rey.
Schem says those costs will scare many boaters away, and he points to a reported $200-million price tag for dredging the marina, all of which he says may be overkill.
"The water board talks about sport fishing, they talk about shell fishing and swimming, and those are three prohibitive uses currently in Marina del Rey," said Schem.
Unger says the cleanup costs being talked about are exaggerated, though he wouldn't give an estimated price. But he calls similar dredging projects like the one in San Diego successful and says biocide boat restrictions are spreading.
"The entire state of Washington up north, they have banned the copper-based paints," said Unger.
Schem says there are currently "no viable non-pesticide bottom paints available for Marina del Rey."