Machias Seal Island, home of the largest puffin colony in the Gulf of Maine, has had the worst breeding season ever recorded, with the vast majority of chicks starving to death in their burrows.

The disaster followed a sudden drop in the puffins’ food supply – certain small fish – in early July, said Tony Diamond, director of the Atlantic Laboratory for Avian Research at the University of New Brunswick, who oversees research on the island’s seabirds. Adult puffins fly out to catch fish to feed their fledglings, which remain behind in burrows, but for the remainder of July and August the parents were returning with little in their beaks, Diamond said.

In a typical year, 60 percent of the puffin nests with eggs produce chicks that fly off in late summer to begin their life at sea. This year the number was only 12 percent – 320 chicks – the worst result since researchers began monitoring the colony in 1995.

“Those that fledged were often very small with lots of down left in their plumage, so I don’t expect … any of the chicks that hatched to survive long enough to breed,” Diamond said.

The island, object of a territorial dispute between the U.S. and Canada, is 20 miles south of Machias and occupied year-round by Canadian lightkeepers. It is home to between 5,000 and 6,000 Atlantic puffin breeding pairs, over five times more than the Gulf of Maine’s other breeding colonies combined.

Atlantic puffins, whose colorful beaks and penguin-like charisma have made them a tourist draw from Maine to Iceland, are a barometer of ecosystem health, since they rely on the availability of forage fish.

Before this summer, the worst breeding year at Machias Seal Island was in 2013. It was the summer after the “ocean heat wave of 2012,” when average surface temperatures in the Gulf of Maine reached the warmest levels ever recorded, disrupting puffins’ food supplies: juvenile white hake, sand lance and herring. In 2013, only 15 percent of chicks survived, but at least those had healthy body weights, Diamond said.

Usually, researchers are able to put identification bands on the chicks in late July or early August, before they leave their burrows. “But we couldn’t this year because the chicks’ legs were too small to hold a band,” Diamond said. “We have never seen fledgling weights like this before.”

A hundred miles to the southeast off midcoast Maine, puffin colonies have fared better, said Cornell University ornithologist Stephen Kress, director of the National Audubon Society’s Seabird Restoration Program. The program has overseen the 40-year effort to restore puffins to three islands: Eastern Egg Rock in Muscongus Bay, and Seal Island and Matinicus Rock, two offshore islands south of Penobscot Bay.

Two of the three islands have had a relatively normal year, although the mix of fish species that the puffins are bringing back to their chicks has been a little unusual. At both Eastern Egg Rock and Matinicus Rock, roughly three quarters of egg-bearing nests have produced fledgling chicks, although the biggest food source has been warmer-water redfish rather than the juvenile white hake and sand lance that typically dominate their diet.

But at Seal Island – a grassy and remote island once used by the Navy for bombing practice – the success rate was closer to 50 percent with no sign of redfish, leading Kress to speculate that the colony suffered because the birds couldn’t access this alternate food supply. Instead, puffins were bringing back northern puffer, a less than nutritive warmer-water species that scientists had never previously seen the puffins eat.

“The puffins head out each morning like a fishing fleet and look for the catch of the day, so each island has its own grounds,” Kress said. “Over the past 40 years, we’ve restored multiple colonies, and that’s really important now for protecting against climate change impacts.”

Diamond suspects puffins at Machias Seal Island may be suffering precisely because their colony has far more mouths to feed. “In a time of food scarcity, the competition for food is much heavier than it is at the smaller islands,” he said.

Puffins were virtually wiped out in Maine in the mid-19th century by hungry fishermen, who threw nets over puffin hideaways to catch them by the thousands. Restored to midcoast islands by scientists, puffins have a threatened status in Maine and were recently listed as endangered in Europe, where Icelanders caught and consumed them as a delicacy just six years ago. Iceland’s big colonies – the country hosts 2.5 million breeding pairs – have been in decline because of food shortages.

Off Maine’s coast, the birds were recovering nicely until recent years. Since 2004, the Gulf of Maine has warmed faster than anyplace else on the planet, except for an area northeast of Japan. Researchers have seen a correlation between warmer waters and food stress in puffin chicks.

This year is shaping up to be the second-warmest on record for the gulf, said Andrew Pershing, chief scientific officer at the Gulf of Maine Research Institute in Portland. As of Monday, the average sea surface temperature across the gulf this year has been 66.2 degrees, 3 degrees above normal. The only warmer year was 2012, when temperatures ran 5 degrees above normal.

The warming has been more pronounced in the eastern half of the gulf, Pershing said, with above-average temperatures recorded down to 150 feet by buoys Down East. The western half has been normal or even slightly cooler than average, which may account for the differing experiences of the puffin colonies, he said.

Fortunately, Pershing said, his colleagues haven’t been fielding questions from the public about strange marine species or armies of jellyfish showing up like they did in 2012.

“The story so far has been how, at least in the coastal areas where most people interact with the oceans, how normal it has been,” he said.

Correction: This story was revised at 6:40 a.m., Aug. 23, 2016, to correct the academic affiliation of ornithologist Stephen Kress, director of the National Audubon Society’s Seabird Restoration Program. Kress is a visiting fellow at Cornell University.