Editor's Note: Expedition Blue Planet, led by Jacques Cousteau's granddaughter Alexandra Cousteau, is traveling 14,500 miles of road over 138 days to investigate and film some of North America's most pressing water-use and management stories. Expedition members will file dispatchs from the field for Scientific American until the expedition concludes on November 12 in Washington, D.C. This is their fifth blog post.

"The microorganisms seem to be disappearing," says Reid Brown, a herring weir fisherman on Deer Island, New Brunswick.

"It means no food for the fish. It's the bottom of the food chain," he says over the growling engine of his 45-foot cape island fishing boat, "Rebecca and Shelley."

Brown is particularly concerned about the herring, which he harvests in weirs, a passive and sustainable traditional fishing structure. "We're having problems this year with sardines not growing. Their fat content is down to 3.5 to 4 percent fat content and usually this time of year they should be up around 14 percent," he says.

In his 47 years of fishing, Brown's seen tremendous changes in the waters that provide his livelihood: "Seems to be more pollution and less sea life."

The changes he's seen in his waters are coincident with the explosion of Atlantic salmon farming in the Bay of Fundy. The farmed fish are hotbeds for sea lice, a salmon parasite that the industry combats using pesticides. But the cumulative ecological effect of these pesticides remains unclear.

Last November, a local lobster kill was linked to the illegal application of cypermethrin, a pesticide that kills sea lice. And just last week, the Canadian government temporarily approved the use of the pesticide Alphamax, which contains deltamethrin, to combat sea lice. Deltamethrin is extremely toxic to crustaceans.

"Whenever you're dependent on chemicals, concern is justified," says Fred Whoriskey, executive director of the Ocean Tracking Network at Dalhousie University in Halifax, Nova Scotia. "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."

We follow the shore north from Leonardsville Wharf and go up into Doctor's Cove where a pack of salmon cages stick out from the water.

"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. She's impervious to the cold wind buffeting around us as we move through the water. "It's the success of one industry at the cost of another," she says.

In 2005, New Brunswick grew over 40,000 tonnes of farmed salmon with global farmed salmon output totaling 1.32 million metric tons in 2009. There are 96 fish farms in the Bay of Fundy, with tens to hundreds of thousands of salmon in each farm.

"These are factory farms on the bay," says Matt Abbott, Fundy Baykeeper coordinator in Saint Andrews, New Brunswick. "Aquaculture isn't just like any other farming. The marine environment is so different than the terrestrial environment."

The sea is choppy and flecked with seabirds skirting its surface. Wings extended, their white, arced bodies mirror the white caps that reach up for the pale blue sky. Inside the boat, heat from the engine is fanned into the little room.

Brown is at the wheel, the smoke from his Export A cigarettes dissolving into the air. He picks his words carefully when talking about his 7-year old grandson, who's intent on fishing.

"He reminds me of myself at his age and I'm very afraid there'll be nothing left for him to know," he says. "There's a lot of stuff that's gone missing here."