A judge has ruled that the Conservation Law Foundation (CLF) can move forward with its lawsuit in Maine against Cooke Aquaculture, one of the world’s largest salmon producers, for allegedly violating the Clean Water Act.
The Canadian company has 13 active sites in Maine, including in Cobscook Bay and Machias Bay, where the company grows millions of salmon.
The company strongly denies the allegations and had filed a motion to have CLF’s suit dismissed. However, on September 30 U.S. District Court Judge Karen Frink Wolf ruled that all but one of the six claims in CLF’s lawsuit could proceed and a portion of that one claim can also be considered by the court.
Concerning the allegation that Cooke is violating the state’s effluent limitations through unlawful discharges, the judge found that two sections of the National Pollution Elimination Discharge System (NPDES) permit issued by the Maine Department of Environmental Protection (DEP) are unenforceable, since they do not explain what Cooke must do to comply with the permit’s provisions. The judge declined to dismiss the portion of that claim that alleges that Cooke discharges pollutants containing materials that are hazardous to aquatic life.
“This ruling brings us one step closer to protecting the health of Maine’s waters and the ecosystems, industries and communities that rely on them,” says CLF senior attorney Maggie Nivison in a release. “These enormous salmon cages are like sewage pipes to the marine environment. Accountability matters, and we need to enforce our laws to safeguard Maine’s bays and communities.”
Most of Cooke’s salmon cage sites are located in coastal communities where lobstermen and fishermen depend on clean and unpolluted water for their livelihoods. Fish feces, uneaten food and uncollected pieces of dead fish fall through the bottom of Cooke’s cages onto the seafloor to form a thick layer of sediment, according to CLF, which alleges that pollution kills food sources for lobster and bottom‑feeding fish, like flounder, cod and haddock.
CLF sued Cooke in 2025 for violations of the Clean Water Act. The environmental advocacy organization alleges that salmon confined to net pens suffer from disease and parasites such as sea lice at an unnaturally high rate.
“These diseases and parasites can spread from the cages to passing wild fish,” the organization states in a release. “In addition, Cooke’s cages periodically develop holes from exposure to weather and predators like seals, which allow caged salmon to escape. When cage raised salmon breed with wild salmon, the genetic fitness of the wild salmon population is diminished.”
CLF states that Cooke’s NPDES permit does not allow the discharge of escaped fish, sea lice, disease or trash, which CLF alleges continues to occur at the salmon pen sites. The organization alleges that Cooke’s net pen sites are discharging effluent in violation of the permit’s sulfide limitation. As for fish escapes, the notice points to the 50,000 salmon that escaped from the Cross Island sites in Machias Bay in May 2023, following a seal attack.
Cooke Aquaculture, though, has previously stated in a release that the allegations “are false, misleading and lack any substantiating evidence.” The company says it is in full compliance with the laws set forth by the Maine DEP, the Maine Department of Marine Resources and its operating permits.
“Cooke’s Maine Atlantic salmon farms are routinely inspected by state regulators and subject to regular monitoring reports. These laws are designed to protect Maine waters as well as Maine’s heritage fisheries,” states the release, which was issued by Steven Hedlund, director of public affairs for Cooke Aquaculture USA.
The release points out that the company’s salmon farms are also routinely audited and certified by third-party sustainability organizations. Cooke was one of the early adopters of the Global Seafood Alliance’s Best Aquaculture Practices third-party certification program.
As part of this independent, voluntary program, all of Cooke’s Maine salmon aquaculture farms, hatcheries, processing plants and feed mills are audited against standards for environmental responsibility, social accountability, animal health and welfare and food safety.
Additionally, Atlantic salmon farmed in Maine is rated as a “good alternative” by the Monterey Bay Aquarium’s Seafood Watch program.
In the release, Hedlund notes that finfish aquaculture has coexisted with fisheries, such as lobstering, in Maine waters for more than 40 years.
“Lobster landings are not negatively affected by Atlantic salmon farms,” the release states. “In fact, lobster gear is set alongside and within aquaculture lease boundaries.”
However, from 2014 through 2024, the Maine DEP did issue 26 warnings and notices to Cooke and reached one consent agreement that imposed a fine for violations of its Maine Pollutant Discharge Elimination System (MEPDES) permit for net‑pen aquaculture. Many of those violations involved failure to meet the DEP’s reporting requirements or exceeding the maximum number of fish per pen. The consent agreement issued in September 2019 imposed a monetary penalty of $156,213.
The Conservation Law Foundation believes that, to comply with the law, Cooke will need to hire more employees and experts to increase its monitoring and inspections, properly maintain and clean its equipment and mitigate the impact on the environment.