Hundreds of millions of young salmon are emerging from rivers along the B.C. coast, beginning a perilous journey that will take them north into the Gulf of Alaska. What happens on that remarkable migration, which most of the fish will not survive, remains one of the greatest mysteries of ocean science.

Intense research is under way to determine where, why and how young salmon die at sea – particularly over the past few years. One theory is that massive mortality is caused by sea lice and that the infestations come from salmon farms. Gary Taccogna, regional manager of aqua culture environmental operations for the Department of Fisheries and Oceans, disputes that. He monitors lice loads in farms and does not see the link that others do.

Circumstantial evidence is strong. Many of B.C.’s salmon farms are clustered in the Discovery Islands, Broughton Archipelago area, a bottleneck at the north end of Georgia Strait, into which migrating wild salmon funnel. High numbers of fish emerge from this area with lice.

And there is scientific evidence. Research in recent years has shown that farmed Atlantic salmon, densely packed in ocean pens, play host to sea lice, which shed eggs that drift with the tide into the surrounding environment.

In 2008, Alexandra Morton, Rick Routledge and Martin Krkosek published a paper that associated salmon farms in the Discovery Islands with sea-lice infestations on wild juvenile salmon and herring.

Ms. Morton, a controversial researcher because she advocates banning open-ocean salmon farms, reported last week that pink and chum salmon in the Broughton Archipelago are heavily infested with sea lice.

She blames nearby salmon farms. But Mr. Taccogna said other factors may be to blame.

He said in an interview that big runs of spawning salmon last year brought additional sea lice to the area. As those wild runs passed farms, there was a spike in lice infestations there.

B.C. salmon farms are required to treat their fish with a pesticide when the louse load reaches three per adult fish. Mr. Taccogna said DFO field teams routinely sample salmon farms to determine lice loads, and the DFO audits have confirmed farms are doing a good job of controlling lice this spring.

“The numbers [of lice] on the farms are staying at the levels they are supposed to stay at. We are not seeing any failure of treatment,” he said.

Mr. Taccogna said sea lice drop off wild salmon as the adults enter fresh water, and it is suspected that the lice survive the winter by latching onto herring and stickleback.

Then in the spring, when the young salmon come flooding out of the rivers, the lice are ready to attach themselves to their preferred host.

A 2008 study by Craig Losos, a master’s student at Simon Fraser University, points out another issue. Mr. Losos found that while stickleback are infected by sea lice, the fish also prey on lice.

“Thus, sticklebacks are more likely to be ‘sinks’ for sea lice than ‘sources,’” he wrote.

Mr. Taccogna advances another possible explanation, saying natural conditions such as high ocean salinity could explain the high lice loads in wild fish this spring.

Whatever the source, the problem appears serious. Ms. Morton reports 94 per cent of young pink and chum salmon in the Broughton Archipelago have sea lice, and predicts a massive population crash. Fraser sockeye smolts will migrate through the area in two weeks and the same fate could await them, she warns.

Ms. Morton and Mr. Taccogna agree ocean conditions favour sea lice this spring. But whether they survived the winter on farmed fish or some other host remains in dispute.

“That’s the million-dollar question,” Mr. Taccogna said.

Answering it could help solve the mystery of what’s killing B.C.’s salmon and shape the future of fish farming in the province. If aquaculture is playing host to and spreading sea-lice epidemics, the push to get pens out of the sea and onto land can only gain momentum.