The Conservation Law Foundation intends to sue a Canadian aquaculture company for what it says are Clean Water Act violations at 13 sites in Maine where the business “grows millions of salmon in 150 cages.”

The group said in a statement on Thursday that Cooke Aquaculture “regularly pollutes Maine’s iconic bays and negatively impacts recreation and the lobstering and fishing industries.”

Cooke Aquaculture responded with a statement Thursday night, saying the CLF’s claims were “false, misleading and lack any substantiating evidence.”

“Cooke is in full compliance with the laws set forth by the Maine Department of Environmental Protection, the Maine Department of Marine Resources and its operating permits,” the statement said.

It is the latest flare up in a long-running clash between the aquaculture industry and environmental advocates and other critics who say Maine’s coastline is being overrun by industrial-size operations that pollute the state’s pristine waters and take valuable bottom from Maine’s iconic, nearly half-billion-dollar lobster industry.

The Conservation Law Foundation is a New England advocacy group with an office in Portland.

“These enormous salmon cages are like sewage pipes to the marine environment,” Heather Govern, vice president for CLF’s Clean Air and Water Program, said in a written statement. “Their solid waste smothers plants and ocean life while disease outbreaks and sea lice threaten nearby endangered wild salmon. We need to enforce our federal laws to protect Maine’s bays and communities.”

The CLF said that “fish feces, uneaten food and uncollected pieces of dead fish fall through the bottom of Cooke’s cages onto the sea floor to form a thick layer of toxic sediment. That pollution kills the food source for lobster and bottom-feeding fish, like flounder, cod and haddock.”

Fish pens owned by Cooke Aquaculture Inc. at Cobscook Bay’s Broad Cove in Aug. 2021. Derek Davis/Staff Photographer

In addition, “salmon confined to net pens suffer from disease and parasites like sea lice at an unnaturally high rate. These diseases and parasites can spread from the cages to passing wild fish.”

Cooke Aquaculture said its salmon farms are routinely inspected by state regulators and audited 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,” the company’s release said. 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.”

The company said that lobstering and fish aquaculture can coexist.

The CLF said that in order to comply with federal 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.”

Dwayne Shaw, executive director of the Downeast Salmon Federation, said in a written statement that “new evidence documenting Cooke’s chronic violations further illustrates Cooke’s ongoing pattern of disregard for the laws of this state. If Cooke wants to operate in Maine, they should start playing by the rules or be hit with larger fines that finally get their attention.”

Staff Writer Katie Langley contributed to this report.