Cooke Aquaculture Pacific has been granted a five-year permit to farm steelhead in Puget Sound and the greater Salish Sea.

The Washington Department of Fish and Wildlife (WDFW) approved the company’s permit Tuesday, allowing Cooke to transition its net pens from Atlantic salmon to all-female, mostly sterile steelhead.

After hundreds of thousands of Atlantic salmon escaped a Cooke net-pen structure in 2017, the company faced some $332,000 in fines over water quality. Following the escapes, the Legislature in March 2018 voted to phase out farming of nonnative fish — including Atlantic salmon in Washington waters.

The company’s pivot to steelhead could allow it to continue operating in Washington waters, something opponents of the fish-farming industry have promised to fight.

Opponents of fish farming are concerned about viruses, parasites and diseases spreading among Cooke’s fish and then to wild or hatchery fish in Puget Sound. They question the structural integrity of the company’s pens, say fish waste causes water-quality issues and worry that an escape would allow the captive fish to reproduce in the wild.

“Disappointed is an understatement,” Brian Cladoosby, chairman of the Swinomish Tribe, said of the state’s decision. “Our salmon and steelhead are on the brink. Potentially introducing more diseases or genetic defects into our native steelhead is very disappointing.”

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Cladoosby said “dire returns” of steelhead from the ocean have disrupted tribal fisheries for years and that the decision risks the species’ local recovery on rivers like the Skagit. He added that Cooke’s infrastructure restricts access to traditional tribal fishing areas.

Cladoosby expressed disappointment that WDFW announced its decision on Wednesday, which is the anniversary of the 1855 signing of the Treaty of Point Elliott, a day many tribes observe.

“They know the significance of the day for us,” Cladoosby said. “Many tribes will be celebrating Treaty Day. This will definitely be put on their radar screen as another devastating impact the state has done to our most precious natural resource.”

In a document justifying its decision, WDFW addressed some concerns. It wrote that state regulation, and required vaccinations, should help mitigate the risk of infection and disease. Raising steelhead represents less risk than Atlantic salmon for introduction of nonnative viruses, WDFW wrote. Using female triploid fish eggs — which are forced to retain a third set of chromosomes  will make the fish mostly sterile, the state agency said. If a net-pen structure were to fail, as one did in 2017, while farming 1 million fish, the state’s models say between 63 and 316 fertile fish could escape and survive to sexual maturity.

Kurt Beardslee, of the Wild Fish Conservancy, said he thinks the state gets the science wrong and underestimates the risk.

“They’re showing how reckless they’re willing to be with our wild salmon,” Beardslee said.

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WDFW will require Cooke to have an escape prevention and response plan, submit to twice-a-year net-pen inspections by a marine engineering firm, immediately report escaped fish, test for diseases before stocking net pens with smolts, provide annual fish health reports and allow WDFW to sample tissue and perform genetic analysis of breeding fish.

The company cannot farm steelhead immediately. It faces more regulatory scrutiny from other state agencies.

Cooke must amend its water-quality permits with the Department of Ecology.

“They have not yet completed the full application,” said Colleen Keltz, a spokeswoman for that department. That permit will go through a public review process that will take at least several months, Keltz said.

At some of its fish-farming sites, Cooke needs new aquatic lands leases from Washington state’s Department of Natural Resources. Cooke is suing over DNR’s cancellation of its Port Angeles lease. DNR also canceled Cooke’s Cypress Island lease.

In a statement Thursday, Cooke noted that it purchased its Washington fish farms in 2016 and has invested to “modernize the operations.”

The company plans to partner with the Jamestown S’Klallam Tribe to one day farm black cod and steelhead at its Port Angeles site.

“We are very pleased the state approved our trout permit and by working together with the forward-thinking Jamestown S’Klallam Tribe, we will continue to provide a fresh supply of healthy seafood and contribute to the local economy,” said Glenn Cooke, CEO of Cooke Aquaculture Pacific in a statement.