The news for the state’s salmon farming industry of late has been unrelentingly bad. First, a federal judge ruled that two of the state’s largest farming operations, Atlantic Salmon of Maine and Stolt Sea Farms, violated the federal Clean Water Act by polluting the ocean with fish feces, food and medicine. Last month, Judge Gene Carter ordered that the companies, both subsidiaries of Norwegian conglomerates, to perform drastic fixes, such as leaving some ocean pens empty for two years and stopping the use of fish with European genes.

The same judge in April ruled against the state and industry groups when he found that two federal fisheries agencies were correct to place populations of wild Atlantic salmon in eight Maine rivers on the endangered species list. Also in May, a fire destroyed much of a hatchery owned by Atlantic Salmon of Maine in Embden, killing 3 million juvenile fish. On Friday, a case of the virus causing infectious salmon anemia was confirmed in a cage at a farm in Cobscook Bay owned by Heritage Salmon. Approximately 28,000 fish were ordered killed.

The news has not just been bad for the industry. Judge Carter also had harsh words for state and federal regulators who let fish farms operate for 13 years without federal discharge permits. In his 47-page ruling, Judge Carter required state regulators and salmon farmers to take more responsibility, through rewritten policies, new tests and procedures, to ensure that fish farms don’t pollute the Atlantic Ocean.

Add to the mix a report by the Atlantic Salmon Federation and World Wildlife Fund that ranked the United States (meaning Maine, since that’s where most of the nation’s Atlantic salmon is grown) second to last for adopting measure to protect wild salmon populations. The United States scored 0.5 of a possible 10 points, according to the conservation groups. The score could be higher if regulations being considered by state agencies, such as pollution elimination discharge permits that will be presented to the Board of Environmental Protection next week, are implemented.

Given all this bad news, it is obvious that salmon aquaculture – which contributes at least $100 million annually to the state’s economy, according to a University of Maine analysis – must change its practices and that state and federal regulators must ensure they do so. A Task Force on the Planning and Development of Marine Aquaculture in Maine, proposed by Gov. John Baldacci, might help, although it will not resolve the many legal issues surrounding salmon farming. The panel, made up of 11 members of the public, some with aquaculture knowledge, some without, will try to balance scenic views prized by residents and tourists with the economic impact of fish farming, especially on economically depressed areas of the state such as Washington County, home to the majority of salmon farms. It will also study the concept of a bay management system whereby the number of farms in a specific area is limited to minimize impacts on the ocean and its other uses.

The task force, however, cannot end all the controversy surrounding aquaculture. Large companies, such as Atlantic Salmon of Maine and Stolt Sea Farms, can no longer try to circumvent the law. The companies should improve their husbandry practices to limit the spread of disease and degradation of the ocean floor. They should also stop using fish with European genes to limit the threat of disease and genetic dilution posed to wild Atlantic salmon by escaped farm fish. These changes will no doubt be costly, but so are lawyers.

Needless legal fights are also the reason Gov. Baldacci should accept the federal court ruling that the endangered species designation was warranted for Maine’s remaining wild fish. An appeal of this decision, which must be filed next week, would be a waste of state time and money.