At least one B.C. fish farm site in Clayoquot Sound was closed this summer as a result of high counts of sea lice, a tiny parasite that occurs naturally in the wild but can flourish in the confined quarters of open-net pens.

Cermaq Canada, a subsidiary of Mitsubishi Corp., closed its Fortune Channel fish farm on Aug. 31 after several weeks of high lice counts at the site, one of 15 the company operates in Clayoquot Sound, off the west coast of Vancouver Island.

Fish at the site were not thriving even after being treated with a hydrogen peroxide-based pesticide earlier in the year, Linda Sams, director of sustainable development with Cermaq Canada, said in a recent interview.

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Ms. Sams said hot, dry weather in the spring affected water quality and contributed to higher lice counts at some Cermaq sites. “We didn’t see these fish recovering well … we have a very strong welfare policy at Cermaq, so that was a key consideration,” she said.

The fish were killed and processed into fertilizer. Employees who worked at the site are now at other locations. Ms. Sams would not say how many fish were at Fortune Channel, saying only that each site typically has several hundred thousand fish and that a “significant number” were involved. The company said the site would reopen in 2019.

It’s not unusual for a site to be temporarily out of production depending on farming schedules, but it is relatively rare for farmed fish to be killed without going to market. B.C. has 116 marine finfish farms; on average, 60 or so might have fish on site at any given time, according to a 2017 Fisheries and Oceans Canada report on the sector.

Sea lice are parasites that occur naturally in the wild and feed on the skin and mucus of fish. In general, they don’t harm larger fish, but as few as two or three can kill a small fish. And sea lice can pose a threat to wild juvenile salmon when they migrate past fish farms on their way from freshwater to the open ocean – a key issue in a debate in B.C. about fish farms' potential impact on wild salmon runs.

Fish-farm operators are required to track sea lice counts and report the numbers to the Department of Fisheries and Oceans.

If counts of farmed fish show an average of more than three moving lice per fish, operators are required to take measures to reduce lice levels by, for example, treating them with pesticide.

Monitoring information posted by Cermaq shows sea lice counts at the Fortune Channel site hit 10.8 per fish on July 10 and were at seven per fish on Aug. 1 before dropping below required treatment levels in early August. The company also reported above-threshold sea lice counts at several of its other sites.

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DFO said it was aware of elevated sea lice levels at some sites in Clayoquot Sound, but had not ordered any closings.

“During most years, more than 90 per cent of [fish farm] sites are below the regulatory thresholds for sea lice during the wild salmon outmigration period (from March 1 to June 30 of each year),” DFO spokeswoman Michelle Rainer said in an e-mail.

Shawn Hall, spokesman for the B.C. Salmon Farmers Association, said he was not aware of any other sites that culled fish this year as a result of sea lice outbreaks.

Cermaq has 28 farm licences in B.C. The company is planning other measures to tackle sea lice in the future, including a $12-million barge that uses seawater pressure to remove the parasites.

Joe Martin, a councillor with Tla-o-qui-aht First Nation, said sea lice are a continuing concern and pose a risk to migrating wild salmon.

“Ever since these salmon farms have been in here, our stocks have not been increasing at all,” Mr. Martin said. “In fact, they have been declining."

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Fish farms are subject to a joint provincial-federal licensing regime. In June, the B.C. government announced that effective June, 2022, the province would grant fish farm tenures only to operators that have satisfied DFO that their operations would not hurt wild salmon stocks and have negotiated agreements with First Nations in whose territory the companies plan to operate.