In North America, Atlantic salmon migrate up rivers and streams to reach spawning grounds in New England and Canada. © Design Pics Inc / Alamy Stock Photo

By the fall of 2015, the salmon of the Connecticut River were supposed to be doomed. The silvery fish that once swam the Northeast’s longest river, 407 miles from the mountains of New Hampshire to Long Island Sound, went extinct because of dams and industrial pollution in the 1700s that turned the river deadly. In the late 1800s a nascent salmon stocking program failed. Then in 2012, despite nearly a half-century of work and an investment of $25 million, the federal government and three New England states pulled the plug on another attempt to resurrect the prized fish. But five Atlantic salmon didn’t get the memo. In November, fisheries biologists found something in the waters of the Farmington River — which pours into the Connecticut River — that historians say had not appeared since the Revolutionary War: three salmon nests full of eggs. “It’s a great story,” said John Burrows, of the Atlantic Salmon Federation, a conservation group, “whether it’s the beginning of something great or the beginning of the end.” The quest to resurrect Atlantic salmon in the Connecticut River began anew in the mid-1960s when the federal government and New Hampshire, Vermont, Massachusetts and Connecticut joined forces. They worked to curb pollution in their shared river and also build passageways around some of the 2,500 dams that plugged the river and its feeder streams in the 11,250-square-mile Connecticut River watershed. The streamlined wild Atlantic salmon, genetically different from their fattened domesticated counterparts, which are mass-produced for human consumption, are so rare that anglers spend small fortunes chasing them across Canada, Iceland and Russia. Robert J. Behnke, the preeminent salmon biologist of the 20th century, wrote that Salmo salar (Latin for “leaping salmon”) has inspired in people “an emotional, almost mystical attachment to a species they regard as a magnificent creation of nature.” Through the Connecticut River restoration program, a few thousand 2-year-old Atlantic salmon raised in a fish hatchery were stocked in the river in 1967. But they all soon died or swam out to sea and never returned. Program leaders knew they needed to survive not just for the sake of the species, but also to get the public to support the program. Before European colonization, biologists estimate, the Connecticut River teemed with annual runs of 50,000 Atlantic salmon, the most in North America. But, as the Boston Globe noted, “the fish had been gone so long there weren’t even great-grandparents who remembered them.” Kenneth Sprankle, a coordinator with the U.S. Fish and Wildlife Service, wrote that the salmon lost their “level of relevance.” All the stocked salmon continued to die off through the early 1970s. Gradually, scientists began to learn the importance of different strains of salmon and their close relatives, trout. In 1976 the program was able to acquire Atlantic salmon eggs from the Penobscot River in Maine, the closest surviving population both physically and genetically. This strain was still different from the lost native strain of the Connecticut River, but less so than their Canadian cousins, previously stocked there. In 1978, 90 fish from the Maine strain managed to make the two-year, 6,000-mile migration out to the food-rich Labrador Sea off of Greenland and then return to the Connecticut River.

‘If you want a dog that jumps in the water, keep breeding ones that do and eventually you’ll have a Labrador retriever.’ Steve Gephard fisheries biologist

In 1981, more than 500 salmon returned — the most yet. Biologists hoped they were on the verge of re-creating one of the most fragile, complicated and increasingly rare natural phenomena on earth, a long-distance animal migration. By the mid 1990s, all of the salmon that found their way back to the Connecticut River were caught and bred at the Richard Cronin National Salmon Station, a fish hatchery in Sunderland, Massachusetts. Their eggs were then incubated at the White River National Fish Hatchery in Vermont. The biologists wanted to use a technique known as reproductive isolation, commonly known as inbreeding, to redevelop a strain of salmon that followed genetic commands to migrate out from and back to the Connecticut River, a facsimile of what nature had done a million years earlier. Stephen Gephard, senior fisheries biologist for the state of Connecticut, compared the process to dog breeding. “If you want a dog that jumps in the water, keep breeding ones that do and eventually you’ll have a Labrador retriever,” he said. The other part of salmon migration, biologists learned, is trained behavior. Salmon remember the isotopes and chemical elements of the waters where they live as juveniles so they can return as adults. Biologists then began stocking Connecticut River waters with the youngest salmon they could in order to give them the maximum environmental imprint. “We knew we were never going to do as well as Mother Nature,” Gephard said. “But that’s what we were trying to do.” By combining reproductive isolation with early imprinting, the scientists increased the rate of salmon returns tenfold from the beginning of the program. One U.S. Fish and Wildlife biologist boasted in the early 1990s that they had achieved a “miracle recovery.” But then wild Atlantic salmon around the world began to die off. So did cod, lobster and winter flounder. Scientists found that capelin, a small fish that salmon feed on in the Labrador Sea, had on average become significantly smaller in size in just a few decades, suggesting that salmon were not finding the calories they needed to survive their migrations. By turn of the 21st century, cycles of ocean currents that had historically made fish populations fluctuate grew erratic and unpredictable. More ominously, researchers found that while much of the Atlantic Ocean had gone up in temperature, around Greenland the water had turned both colder and less saline — symptoms consistent with the theory that the ocean was changing because of global warming. “Things are really variable now,” said John Kocik, a fishery biologist for the National Oceanic and Atmospheric Administration.

Mickey Novack, hatchery manager at Cronin National Salmon Station, with a female Atlantic salmon that returned to the Connecticut River in the spring, now in a giant hold until the fall. Joanne Rathe / The Boston Globe / Getty Images

In 2001, only 40 Atlantic salmon returned to the Connecticut River. The next year there were 44. The George W. Bush administration cut the budget of the U.S. Fish and Wildlife Service and some Atlantic salmon restoration proponents began to question whether the anemic returns justified the annual cost of around $2 million — tens of thousands per fish. Meanwhile, the general public mostly ignored the program, because the salmon had not yet returned in large enough numbers to be seen or caught. What happened next, Gephard said, was “a perfect storm.” Hurricane Irene, its gale winds pulling extra energy from the warmed waters of the mid-Atlantic, wrecked the White River National Fish Hatchery in Vermont in August 2011. The damage to the facility, where 65 percent of all Connecticut River Atlantic salmon eggs were raised, was estimated at as much as $14 million. As only 54 salmon returned to the Connecticut River in 2012, the U.S. Fish and Wildlife Service pulled out of the restoration program. New Hampshire, Vermont and Massachusetts followed. Connecticut opted to continue stocking a small number of salmon, but it lacks the resources to continue the breeding program, which had made such progress. While the restoration program failed for salmon, it boosted a suite of other species. American shad, gizzard shad, sea lamprey, striped bass, sea-run brown trout, white perch, alewives, yellow lamp mussels and endangered American eels in the Connecticut River all jumped in population. Then in the fall of 2015, biologists found five adult Atlantic salmon swimming past the Rainbow Dam on the lower Farmington River. On a hunch, they searched likely upstream spawning habitat and there found the three nests full of eggs. In the spring of 2016 they will hatch the first wild salmon into that river in two centuries. (In 1991 a few salmon spawned for the first time in centuries in Connecticut’s nearby Salmon River.) The phenomenon was so extraordinary that the nest’s location was kept a tight secret. Some local fishermen refuse to even speak about them for fear attention might do them harm, and some state officials even opted for plausible deniability. “I don’t know where they are, and I really don’t want to know,” said Neal Hagstrom, inland fisheries biologist for the state of Connecticut. “Sometimes it’s better that way.”