The Connecticut River was one of the southernmost--if not the southernmost--river that held salmon in historical times.  You have to wonder whether the loss of the strain that were originally native to the river, and maybe a particular genetic adaptation that allowed the fish to thrive in warmer water, doomed the effort from the start, particularly when coupled with the upward trend in water temperatures that has been occurring in recent decades.
One thing that we can never lose sight of is that salmon are not fungible; each "run" has been genetically tuned to optimize survival and reproduction in a particular river, and in its season of return (this is particularly true of Pacific salmon, with their much wider distribution on the west coast of North America).  Lose a run, and you can never really replace it with hatchery fish that originated elsewhere.  Only millenia of evolution can make a salmon truly fit for its natal stream.  Trying to restore salmon to a river system is a noble and probably worthwhile effort, but in the end it is likely simpler, and more cost-effective, to do what needs to be done to avoid destroying the native runs in the first place.

The Canadians can restore all kinds of salmon rivers because each river has a few native fish to work with.  One point my friend Dr. Ray White made a few years ago that got the Maine bios in high dudgeon because they knew it was true is that if no hatchery salmon had ever been dumped into the Penobscot, restoration would now be way ahead of where it is because there have always been a few native fish in that river.  I think the tragedy of shutting down the CT program is that we were near to “recreating” a fish suited to the CT via fast-track selection.  It took a couple centuries to wipe them out; and we sought to restore them in a few decades.  Here, from the winter 2003 Patagonia Catalogue, is my two cents on the issue.  I can’t see anything I’ve changed my mind about in the succeeding nine years.

Everything But Salmon

by Ted Williams

The 407-mile-long Connecticut River dwarfed the continent's other Atlantic salmon streams. Each spring, shoals of salmon, strung like stars across the vastness of the North Atlantic, moved from their rich feeding grounds off Greenland into Long Island Sound, then surged upstream. Through Connecticut, Massachusetts, Vermont and New Hampshire, they veered off into tributaries, climbing high into the Green Mountains and White Mountains, hurdling over falls, waiting out summer droughts, spawning under gaudy leaves, holding through winter, sweeping back to the sea on spring floods. 

Then, in 1798, the Upper Locks and Canal Company blocked this ancient migration with a 16-foot-high dam at Turners Falls, Massachusetts. Pollution and more dams followed, and within a few years Connecticut River salmon were extinct. Fish ladders and fry stocking in the 1870s and 1880s failed. 

A second restoration attempt was just underway in 1970, when I signed on as wildlife journalist with the Massachusetts Division of Fisheries and Wildlife. Quoting state and federal biologists, I assured the public that the Connecticut River system would sustain "thousands" of salmon within a decade. Today, it sustains about seven million. Unfortunately, they're fry-stocked by the four states and the U.S. Fish and Wildlife Service. Annual returns of adults in 2001 and 2002 were 40 and 44, respectively. 

Something has gone dreadfully wrong with Atlantic salmon restoration, but not in the river. Juvenile salmon thrive in freshwater, then vanish at sea. It's happening not just to Connecticut River fish, but to the species throughout its range. Satellite imagery reveals drastic cooling of ocean habitat. One favored theory attributes the cooling to runoff from the melting ice cap. 

Among anglers, impatience has turned to pique. For example, the Lawrence (Massachusetts) Eagle-Tribune's respected outdoor columnist, Roger Aziz, charges that Atlantic salmon restoration "is perhaps second only to [Boston's] Big Dig in wasteful spending of other people's money." He suggests that funds go instead to more trout stocking, and he scolds managers for endangering upstream game fish by not killing all the parasitic sea lamprey when they're in the fish lift at Holyoke, Massachusetts. 

Meanwhile, restoration is being defunded by the Bush administration to the point that some hatcheries and holding facilities don't have money to feed fish or even pump water.

But critics ignore the fact that while New England waited for salmon, a whole ecosystem quietly came alive. In 1970, managers argued about whether to call the program "anadromous fish restoration" or "Atlantic salmon restoration." Hoping to capitalize on the mystique of Salmo salar, they opted for the latter. They used the program to leverage clean-water standards as well as upstream and downstream fish-passage at six main-stem dams and seven tributary dams. 

Steve Gephard, Connecticut's anadromous-fish chief, keeps his boat moored on the river where he grew up, in Haddam, Connecticut. "The river reeked in the late 1970s," he recalls. "It would change color according to who was dumping what, and we'd have regular fish kills." Now there are no fish kills, and what he smells is the fragrance of salt marsh, tidal flat and sun-baked driftwood. He can see his toes when he wades chest-deep to his boat. 

With the 44 salmon in 2002 came 377,420 American shad, 3,054 gizzard shad, 77,430 sea lamprey and 1,950 blueback herring. This was the smallest herring run since accurate records began in 1976, but apparently for a happy reason. In the reborn river below Holyoke, herring are being swilled by an estimated 1.5 million striped bass. Other migratory fish such as white perch, alewives, sea-run brown trout and American eels are thriving. Endangered shortnose sturgeon are on the rebound. 

The alewife floater mussel, which had been excluded by dams because its larvae hitch rides on alewives and related species, are reappearing in old haunts. So are yellow lamp mussels and tidewater muckets, which attach themselves to white perch and probably striped bass. Mussels, particularly the thin-shelled alewife floater, are relished by raccoons, muskrats and otters. 

In sterile, glaciated woodland ponds and streams, the huge influx of nutrients from the sea in the form of fish carcasses, feces, eggs, milt and young has restored a host of native insect fauna, which in turn, has nourished fish. Sea lampreys, native Yankees which threaten no marine fish, go blind on their spawning run and can't feed. They make nests with their sucker mouths, clearing pebbles and shaking out sediments; then they all die. The clean bottom attracts spawning salmon. Lamprey carcasses feed caddisfly larvae, which are then eaten by trout and young salmon. If the whole is beautiful, no part can be ugly.

Non-migratory fish are surging back into newly clean, newly fertile habitat, and with the explosion of fish has come stunning increases in ospreys, eagles, mergansers, kingfishers and herons. 

About the only thing missing from the Connecticut River system are healthy runs of Atlantic salmon. As discouraging as this may be, the rebirth of the river's ecosystem has given salmon restoration a chance it never had, provided marine habitat improves. The few salmon that are returning are genetically distinct from their principal ancestors fish from Maine's Penobscot River that were stocked in the 1970s. The difference could be the result of crossbreeding with introduced stock from other rivers. Or it could mean that in barely more than 30 years, nature, with human help, has created something Earth had lost: a race of Atlantic salmon precisely suited to the Connecticut River. If this latter theory is correct, and studies support it, managers at last have the spark to rekindle a dead fire. 

The Connecticut River's Atlantic salmon may not be doomed. If the black hole they're falling into at sea turns out to be a temporary phenomenon, and if there's really a new race of salmon honed and polished by perhaps the fiercest natural selection the species has ever known, there's a good chance that salmon restoration will finally succeed. Now is the worst possible time to let the spark flicker out.