We are as close to the salmon cages as we can get, telephoto lenses out, video rolling. From our vantage point, fisherman Reid Brown's 45-foot boat the Rebecca and Shelley, we don't see any salmon but the seabirds clamoring around the raised salmon cages are excited about something here in Passamaquoddy Bay on the Bay of Fundy.

This region is throne to a wealth of wild marine diversity and biomass, a bounty that is augmented (and unseated in the opinion of some) by booming salmon farms. There are 95 salmon farms in New Brunswick's waters that produce 26,000 metric tones of salmon each year. Together they stock enough smolt, roughly 12 million, to outnumber people in New Brunswick 16 to one.

The waters that Brown has fished for 47 years show signs of malcontent. "The microorganisms seem to be disappearing, zooplankton and so on," says Brown. "Means no food for the fish." It's unclear whether the drop in zooplankton is linked to salmon farming but other connections are more obvious, such as the lobster kill last year traced to an illegal chemical that kills sea lice, the bane of salmon farmers.

Expedition Voices: The Legacy of Atlantic Canada's Salmon Farming from Alexandra Cousteau on Vimeo.

Some 30 years into the relatively new practice of fish farming the debate continues: What ecological toll does salmon farming exact on the greater marine environment, and how can salmon aquaculture proceed sustainably?

What began as chemical warfare to quell sea lice numbers in salmon farms has turned into an arms race as the parasitic crustaceans, which attach to salmon and increase their susceptibility to disease, have developed resistance to treatments. As the chemical ante is upped, so too are concerns about ecological side-effects.

"The kinds of chemicals you need to kill sea lice are not specific only to sea lice. They also affect crabs and lobsters and also copepods, so there's great concern about that," says Fred Whoriskey, executive director of the Ocean Tracking Network at Dalhousie University in Halifax, Nova Scotia. Go to the bottom of any marine food chain and you'll find the likes of crustaceans, such as krill and zooplankton, for which deltamethrin (the main ingredient in AlphaMax, an anti-sea lice pesticide recently used on salmon farms in New Brunswick) is highly toxic.

"If the status quo remains it's going to harm and kill marine ecosystems," says Matt Abbott, Fundy Baykeeper coordinator in Saint Andrews, New Brunswick.

Emergency pesticide treatments halted

Recent deltamethrin (marketed as AlphaMax) sea lice pesticide trials in the Bay of Fundy were halted after preliminary experiments by Environment Canada resulted in dead lobsters in and round the plume of pesticide.

Environment Canada Media Relations Advisor Henry Lau emailed this statement: "Testing was conducted to monitor the application of Alphamax using a tarp system to confirm that this application is in compliance with the Fisheries Act. Preliminary results have raised some questions about the currently-proposed tarp application system, and these results are being reviewed by all parties."

"I did hear that these lobsters died and I am frankly not surprised because we know that deltamethrin can be harmful to lobster, which is why we have designed these systems so that the lobster will not come into contact with the product," says Pamela Parker, executive director of the Atlantic Canada Fish Farmers Association.

Salmon farmers raise their nets to apply the pesticides. The fish then soak in the pesticide solution, which is later released into the estuarine or near shore habitat. While it is true that grown lobsters live on the ocean floor, critics point out that lobster larvae concentrate near the water surface where the pesticides are, and are far more sensitive to lower concentrations of the pesticide. Furthermore, sediments are a major sink for deltamethrin in freshwater ponds, which suggests that it may incorporate into ocean sediment as well.  

The recommended dosage of deltamethrin to rid farmed salmon of sea lice is three parts per billion for 40 minutes . Even if this concentration were diluted by a factor of 82 it would still kill 50 percent of stage III lobster larvae exposed for one hour, according to a 2009 Department of Fisheries and Oceans (DFO) report published by the Oceans and Science Branch in Moncton, New Brunswick. If the recommended dosage were diluted by a factor of 230 it would still be deadly to half of the amphipods, tiny crustaceans critical to marine food webs, exposed for one hour.

"It will dissipate very quickly in the marine environment," says Parker, based on unpublished experiments that the salmon growers association conducted last year. "The active ingredient deltamethrin was undetectable outside the net pen skirting during the trial and within ten minutes following the release of the skirting."

Counter to this, the study authors conclude that the recommended dosage of deltamethrin will impact crustaceans over 100 meters away from the net pens for 2-4 hours following treatment based on their findings. Furthermore they report that the amphipods were so sensitive to the pesticide that they couldn't establish the threshold toxicity value for immobility.

"I find it very disturbing that the federal and provincial government will pass these chemicals because they are against [articles in] the Oceans Act… to dump lethal chemicals in the water," says traditional fisherman Reid Brown. "If I dumped them in the water I'd be in jail."

Do salmon farms come at the expense of lobster nurseries?

One of cameraman Christoph Schwaiger's best birthday presents was a fresh lobster proffered by our hosts for the night, the Ross family in Saint Andrews, New Brunswick. His birthday lobster (briefly named Lisa) was black and shiny, speckled with carmen red, and the lobster meat was absolutely delicious, equal parts succulent, sweet and briny.

It wasn't until later, after we spoke with local fishermen and scientists alike, that we learned about the deleterious effect of salmon farms on lobster fisheries.

"You see the salmon cages over top of known lobster nurseries or scallop beds," says Sheena Young, program coordinator for the Fundy North Fisherman's Association from the deck of the Rebecca and Shelley. "It's just devastating."

"It's suicide to the lobster fishery to be dunking those chemicals in," says Mike Strong, a retired surveys biologist for the Department of Fisheries and Oceans in Saint Andrews, New Brunswick. "The lobster fishery is worth about as much as the salmon- growing industry and to displace a perfectly healthy good fishery by growing salmon, to me it's wrong."

Strong's research revealed that lobsters are in fact very picky about the type of ocean floor they inhabit. "But the problem is that exactly matches what the fish farmers are looking for in terms of establishing cages," he says. "As soon as you put in a fish farm that bottom is no longer suitable for settlement of lobster larvae because all the feces from the fish and the unused food goes down and clots up the bottom."

The relationship between wild and farmed salmon

Salmon farming is still a relatively new practice, having started 30 years ago but already about 60 percent of salmon consumed worldwide are farmed , with annual production exceeding one million metric tons.

For Abbott, to call salmon aquaculture "farming" is a misnomer. "Aquaculture isn't just like any other farming," he says. "It's farming carnivores in the water. It's a totally different equation."

To grow one pound of farmed salmon requires roughly three pounds of wild caught fish. "It takes wild fish to grow farmed fish. That's the key rub," Abbott says. In short, these farms use up much more fish flesh than they produce and therefore cannot replace capture fisheries.

The truth is that wild Atlantic salmon stocks have plummeted in North America – all the way down to 4 percent of what the original production capacity was, says Whoriskey. And in the Bay of Fundy wild salmon stocks have been especially hard hit, plunging from 40,000 returning fish down to a couple hundred in the span of two decades.

No direct causal link between the reduction in wild salmon stocks in the Bay of Fundy and the boom in salmon farms has emerged yet but a study of wild salmon stocks worldwide reports a 50 percent reduction in the survival of wild salmon associated with salmon farming.

Here in the tight-knit communities of New Brunswick however, different fisheries that all draw upon and affect the marine ecosystem – whether they're for wild salmon, lobster or farmed salmon – don't function as zero sum competitors because the larger community remains the strongest common denominator.

"We have met the salmon farmers and they are us. This is not an evil group, they are local people, they are part of the working waterfront," says Whoriskey. "In my opinion again in an ideal world, an industry that's dependent on growing Atlantic salmon is dependent on pristine conditions."