GLOUCESTER, Mass. – A full net breaks the ocean’s surface, and its slick, flashing contents spill on deck. Some fish squirm and flop. Much of the catch is already dead.

The fisherman was after flounder, but he’s also hauled up the coveted codfish. But these cod, valuable as they are, can’t be sold at local markets. They’ll be dumped into the ocean, a resource turned into trash.

A fisherman is supposed to catch fish, but if he’s reached federal limits for a certain species, such as cod, he must throw it away.

That “bycatch” – fish caught unintentionally – is a huge problem, fishermen say, not to mention unspeakably frustrating. One study estimates fisherman throw back up to 48 percent of their catch.

“It kills us,” said Gloucester fisherman Russell Sherman. “It makes you sick. It makes you sick to your stomach.”

But regulators say to protect vulnerable stocks they must limit what fishermen can bring in, even if it means accepting some waste. The alternative is completely closing fishing areas, which would cripple the industry.

“Are there better ways?” said National Marine Fisheries Service spokeswoman Teri Frady. “There could be a better way, but that has not been presented.”

Researchers at the Manomet Center for Conservation Scientists on Cape Cod hope to change that. Manomet scientists are visiting fishing ports in New England and New York, talking to fishermen about possible solutions, such as changing fishing gear and habits.

Their study, funded by a $70,000 federal grant, will be presented to federal managers in late March.

“We want to keep fishermen bringing in a product, but do it in a manner that’s sustainable,” said Gregg Morris, a Manomet researcher.

Bycatch is a global problem, but uniquely urgent in New England because overfishing has left so many stocks in precarious positions.

The codfish, New England’s most important and perhaps most troubled fish, drives bycatch reduction efforts. But fishermen, who met recently in Gloucester, said nearly any species, from flounder to monkfish, poses a bycatch problem.

New England waters add an obstacle to reducing bycatch because different species swim together, and fishermen can’t target one fish without pulling up a slew of others.

Even within New England, the problem varies. Fishermen in George’s Bank, for example, are allowed 2,000 pounds of cod per day, while the limit is 400 pounds per day in the Gulf of Maine. Gloucester fisherman Paul Vitale says he can sometimes reach his limit “in five minutes.”

The limit isn’t always enough to make a trip profitable, so fishermen keep fishing for other species. Every cod unintentionally caught from that point is wasted.

Fishermen have an easy fix to the problem: Let them sell what they catch. “You can sell just about anything you bring up,” Sherman said. “The only thing stopping us is the trip limit.”

Getting rid of catch limits won’t work, according to John Williamson, a member of the New England Fishery Management Council, which helps set regulations.

If fishermen were allowed to keep the protected fish they pull up, they’d inevitably go after it, and vulnerable stocks could be damaged further, he said.

Catch limits are currently the best solution, he said, short of completely locking fishermen out of the fishing grounds. Ultimately, he said, the solution lies with gear changes.

Manomet’s Glass agrees. With a better understanding of fish behavior and habitat, a low-tech tool like a net can be used to selectively pick certain fish out of a crowded fishery, he said.

“It is possible,” Glass said. “It may seem way too futuristic, but it is possible.”

Net design can be manipulated, using different mesh sizes, shapes and colors to allow certain fish to escape, he said.

One experimental net is equipped with a black tunnel, which fish are reluctant to swim through, instead moving upward through mesh which allows smaller, younger fish to get out.