In 2012, the IHN virus infected thousands of salmon farmed in net pens in Puget Sound. Now, the Wild Fish Conservancy intends to sue the EPA and NOAA if action is not taken to develop stricter rules governing large net pens.

"They ended up pulling a million pounds of Atlantic salmon out of those pens, but those fish stayed in the water for almost two months, and during that time they're shedding huge amounts of viruses into the water," explained Todd Sandell.

Sandell is an ecologist who studies fish disease for Wild Fish Conservancy. They've released a notice of their intent to sue the the government, they say, for not taking the risks of fish farms seriously.

"If NOAA says there's not a problem, then Fish & Wildlife goes about their business," Sandell said.

Sandell believes the IHN virus outbreak in 2012 hurt wild salmon. The high concentration of fish in net pens amplified the spread of disease at a time of the year when juvenile salmon were in close proximity.

"And the native fish have to migrate through those pathogen plumes," Sandell said. "They can get infected. Potentially, they can get killed by the virus."

Right now, the EPA and NOAA consider fish farms to have essentially no negative effect on wild fish.

The Wild Fish Conservancy strongly disagrees, pointing out that Chinook salmon and steelhead are both listed as threatened species. WFC argues that the net pens endanger critical habitat after millions of tax dollars have been spent to rehabilitate habitat across Puget Sound.

"So it calls into question whether it's wise to permit an industry that might be undermining that investment – that public investment," Sandell said.

Some fish researchers believe farmed fish disease impacts are minimal compared to the viruses wild fish face everyday.

"No question, net pens can amplify pathogens," said USGS Fish Health Section Chief James Winton. "Whether its important relative to billions of virus particles coming out of the wild fish is debatable."

WFC is also suing NOAA over the effects of hatchery steelhead on wild populations. The litigation has forced the planting of hatchery steelhead in lakes instead of rivers for two years, where the fish are unable to migrate to open waters and grow. Some died due to a lack of food.

The EPA and NOAA have 60 days to respond before WFC plans to take legal action. Neither would comment on any pending litigation.