Atlantic salmon did not disappear from New England rivers overnight. Rather, North American populations of this resilient fish beloved by anglers for its fight and by food aficionados for its flavor have suffered what some describe as “death by a thousand cuts” over the past two centuries.

Most involved in the plight of the Atlantic salmon say industrialized New England’s love affair with hydropower inflicted the deepest, most debilitating wound to the Salmo salar, the species’ Latin name, meaning “the leaper.” Experts often debate where all of the other factors – and there are many – should fall on the blame list.

Below are many of the top obstacles to recovery, what is being done and what some insist still needs to be done to ensure that history books are not the only place future generations of Mainers can find wild Atlantic salmon.

Dams

By the 1800s, there were thousands of dams powering mills and supporting the booming logging industry along Maine rivers. These dams often blocked salmon, shad and other sea-run fish from swimming back upstream to their spawning grounds, or water wheels chewed up fish headed downstream.

Many dams have since been removed or succumbed to nature, while others were updated with “fish ladders,” elevators and other devices that allow fish passage. But many more – 750 at last count, not including old log-driving dams and the smallest dams – still impede natural fish traffic and, therefore, limit recovery.

“There are lots of culverts and little old dams that need things done to them,” said Joan Trial, the Maine Atlantic Salmon Commission’s leading biologist.

In the fall of 2003, parties involved in salmon restoration announced a plan that they predict could rapidly and dramatically reverse population declines in the Penobscot River. The Penobscot River Restoration Agreement calls for the removal of the Veazie and nearby Great Works dams and construction of a fish bypass at a third dam in Howland.

In return, the dams’ owner, power generation company PPL Corp., will not face relicensing opposition from groups involved in the agreement and was allowed to increase generation at other dams.

Patrick Keliher, executive director of the salmon commission, recently called the river restoration pact “the single most important thing to happen for Atlantic salmon” in recent history. “Each time you remove a barrier, you are going to improve the survivability,” Keliher said.

Top federal officials have also hailed the agreement as a national model of “cooperative conservation” because it brought together so many groups, including local, state and federal officials, local and national environmental organizations, the Penobscot Nation and sporting groups.

But fundraising for the initial $25 million to buy the dams has gone more slowly than organizers would prefer. Project organizers have recently stepped up calls on the federal government to fund its share of the bill.

Ocean mortality

It’s known as the “X-factor” in salmon restoration.

In recent years, salmon mortality rates in the Atlantic Ocean have increased markedly, and fish biologists are struggling to figure out why. The fear is that, even if conditions in New England’s freshwater salmon nurseries improve dramatically, wild salmon could still become extinct due to plummeting survival rates in the ocean.

Kevin Friedland, a biologist with the National Marine Fisheries Service in Narragansett, R.I., is among those leading the charge to find explanations for the mysterious die-off. And although the final verdict is still out, Friedland suspects that recent warming trends in the ocean could be a major culprit.

Friedland and his colleagues found a correlation between springtime surface temperatures in the Atlantic and survival rates among salmon smolts making the transition from fresh water to salt water. As surface water temperatures rise, so too do mortality rates among smolts.

The researchers say more study is needed but offer a variety of possible explanations in a 2003 report published in the Canadian Journal of Fisheries and Aquatic Sciences.

Higher ocean temperatures could affect the abundance of the bugs, larvae and other edibles that salmon need to put on pounds and muscle in the ocean environment. Changing thermal conditions could bring different predators into the smolts’ nurseries. Or smolts could simply be expending more energy trying to find areas of the ocean with their optimal temperature.

The researchers also suggested that smolts’ timing could be off and that they are entering the ocean at the wrong time.

In an interview, Friedland said he is unsure if global warming is causing water temperatures to rise in the areas used by the smolts. “We do have some evidence that climate change may be affecting salmon” in the oceans, he said.

Overfishing

Of all the predators salmon face in both the oceans and freshwater streams, the most formidable is clearly man.

Maine’s American Indian tribes may have depended on salmon as a major food source for millennia. Frank Speck, author of the book “Penobscot Man,” called the annual salmon spearing “one of the great seasonal events” in the life of the Penobscot tribe. He described men of the tribe fishing on the rocks just below Indian Island.

“Unheard-of quantities were taken here by the tribe each year until the dam [below Indian Island] was built,” Speck wrote in his authoritative 1940 book on Penobscot life and culture. “In those days they feasted on the fresh fish and smoked a large amount of it for winter upon pole racks over a fire.”

European settlers had the biggest impact on salmon, first by damming the rivers, and then by catching thousands of the remaining fish.

In 1880 alone, fishermen using weirs and gillnets caught more than 10,000 salmon in the Penobscot River, according to Ed Baum’s 1997 book, “Maine Atlantic Salmon: A National Treasure.” Populations began to decline soon thereafter, but the commercial fishery in the Penobscot remained open until 1948.

Fly fishing became popular in Maine rivers in the mid- to late-1800s. Anglers typically took hundreds of salmon in any year, but landings spiked around 1980. Between 1980 and 1986, anglers reported catching and keeping nearly 3,800 salmon in Maine rivers, according to Baum.

The salmon fishery became catch-and-release only in 1995 and was closed altogether in 1999.

But it was not until the discovery of salmon grounds off the coasts of Greenland, Canada and the Faeroe Islands that commercial fishing began taking its biggest toll on Atlantic salmon populations.

Commercial fishermen caught an estimated 1 million adult salmon off the coast of West Greenland annually in the 1970s plus an estimated 400,000 salmon off the coast of Canada.

Canada ended all commercial salmon fishing, except subsistence fishing for native tribes, in the 1990s. And after years of negotiations, commercial fishing off the coast of West Greenland was banned in 2002.

Pollution

Paper mills, factories, town sewage systems and countless other sources large and small once discarded untold amounts of pollutants into Maine’s rivers.

Tougher environmental regulations enacted in recent decades, such as the federal Clean Water Act, forced many polluters both past and present to reduce toxic discharges and to clean up Maine waterways.

But pollutants such as polychlorinated biphenyls, or PCBs, and mercury can linger in river bottoms for hundreds of years, poisoning the entire food chain. And every year Maine’s waterways receive more dosages of toxins in the form of acid rain and runoff of pesticides and fertilizer from farms and lawns.

Adria Elskus, a research fishery biologist and toxicologist with the U.S. Geological Survey in Orono, said there is no “smoking gun” that may be inhibiting recovery of Maine’s salmon populations.

Rather, she and other researchers are concerned about the combined effect of so many chemicals that individually may not pose a risk to salmon health. The fear is that, even at lower levels, these toxins may team up to have a what’s known as a “multiple stressor” effect on the fish.

For instance, acid rain from air pollution lowers the pH of river water. More acidic water also draws more aluminum out of the soil. That combination may make fish more susceptible to certain pesticides from blueberry farms or other agriculture operations.

“We know pesticides are bad, we know low pH is bad, and we know aluminum is bad,” Elskus said. “But we don’t know the cumulative effect at low levels.”

Aquaculture

Ironically, North America’s total population of Atlantic salmon has actually skyrocketed in recent decades. The problem is that the vast majority of the fish are not wild.

In 1998, aquaculture farms growing salmon for human consumption raised nearly 30 million pounds of Atlantic salmon in pens in Maine waters. That number fell to 11.6 million pounds last year because of disease outbreak and lawsuits.

But the only salmon farm operator in the state, Canadian-based industry giant Cooke Aquaculture, recently announced plans to invest $60 million over the next 18 months in its Maine operations. While good economic news for Down East communities, aquaculture’s expansion has implications for Maine’s wild salmon populations.

Salmon farms packed with hundreds of thousands of fish are more susceptible to disease outbreaks, particularly the dreaded infectious salmon anemia. Critics contend that wild salmon can contract the disease either by passing close to an aquaculture pen or through contact with an escapee from a fish farm.

Fish farms also struggle to control sea lice, a parasite that can sap fish strength and transmit diseases. Escapees that find their way to a spawning river can also interbreed with wild salmon, potentially diluting the gene pool.

Last November, tens of thousands of farm-raised salmon escaped their pens off the coast of New Brunswick and disappeared into Passamaquoddy Bay after an apparent act of sabotage. Just this week, Atlantic Salmon Commission staff reported that four aquaculture escapees were caught in the Dennys River.

Samantha Horn-Olsen, aquaculture policy coordinator with the Maine Department of Marine Resources, said Cooke has been controlling outbreaks of salmon anemia in its Maine pens. Officials in Maine and Canada are also beginning a new partnership to cooperatively manage farm operations in some joint waters, she said.

Aquaculture facilities in Maine are also required to report to state officials within 24 hours when older or a larger number of fish escape. Unfortunately, Horn-Olsen said, Canada does not have similar reporting requirements.

“Our regulations are some of the most stringent in the world,” Horn-Olsen said. “If we can responsibly grow … a product that is consumed here, it just makes sense to me.”

Global warming

Some scientists have an unconventional and controversial theory for why salmon are disappearing from New England’s rivers: They suggest things may simply be returning to normal.

In an argument that runs counter to popular perceptions of pre-Colonial rivers chock full of salmon, several researchers have said that archaeological evidence hints that Salmo salar may have only been short-term visitors (geologically speaking) to New England.

Former University of Maine scholar Catherine Carlson found plenty of fish bones but few from salmon during archaeological excavations of American Indian sites throughout New England that dated to before 1500. She then theorized that salmon only became abundant when a 350-year-long cold spell, known as the Little Ice Age, made the region’s rivers cold enough for salmon to thrive.

The Little Ice Age began around 1450 – not long before European arrivals began reporting rivers filled with spawning salmon. It ended around 1800 – about the same time that New Englanders began noticing population declines.

George Jacobson, a professor of biological sciences with UMaine’s Climate Change Institute who has expanded on Carlson’s research, said there is ample evidence that the climate in Maine and New England was historically drier and warmer before 1450.