PORTLAND – The owners of two of Maine’s largest salmon farms went on trial in federal court Tuesday in a closely watched case that could result in tighter restrictions on the state’s salmon farming industry.

Atlantic Salmon of Maine and Stolt Sea Farm were found in July to have violated the federal Clean Water Act by failing to obtain permits to discharge feed, pesticides and other potential contaminants into the coastal waters where their salmon pens are located.

The bench trial that began Tuesday will determine what, if any, financial penalties the companies should pay, and what operating rules they should be required to follow in the future.

Conservationists will push for tighter controls they say are needed to protect coastal waters and help endangered wild salmon.

Officials of Atlantic Salmon and Stolt Sea Farm have said the restrictions sought by environmentalists – including a ban on European strains in cultivated fish – would make it impossible to compete in the global market.

The trial before U.S. District Judge Gene Carter is expected to last five days and conclude next week.

The case dates back to July 2000, when the U.S. Public Interest Research Group filed suit against Atlantic Salmon of Maine, Stolt Sea Farm and Heritage Salmon for discharging pollutants without permits.

Bruce Merrill, a Portland lawyer who represents PIRG, said the group would ask Carter for a range of operating conditions, including public notification whenever the companies put antibiotics in the water.

But the most intense dispute will be whether the companies can continue to use eggs from fish that have been selectively bred in Europe to grow quickly in captivity. The European strain was created over a period of 25 years and is used by salmon farms around the world.

Dave Peterson, chief executive officer of Fjord Seafood USA, which is the owner of Atlantic Salmon, declined to discuss details of the dispute. “We want to present our information in an orderly manner and let the chips fall,” he said.

Heritage Salmon settled its part of the lawsuit in June by agreeing to pay $375,000 to save wild salmon and to follow new operating rules, such as limiting the densities of its fish pens and limiting uses of antibiotics and chemicals.

The company also agreed to use only North American genetic strains to breed its fish, and it said it expected to be successful under the conditions of the settlement.

Heritage Salmon’s agreement should show the other companies that they can use North American broodstock and still be competitive, Merrill said. And, he said, the concerns for wild salmon go back many years, providing the industry plenty of time to develop alternatives to the European strain.

Maine’s $100 million salmon farm industry began about 15 years ago, but federal and state regulators never forced salmon farming operations to obtain Clean Water Act permits.

Atlantic Salmon even applied for the permits, but never got them, Peterson said. “We have done everything our regulators have asked us to do,” he said.