Another possible cause, Pershing said, is that shifts in the Gulf stream, the Atlantic current that originates in the Gulf of Mexico and keeps Europe mild, warmed the ocean off the Northeast.
The Gulf of Maine's temperature is expected to rise more than 4 degrees by the end of the century, Pinsky said.
The 99 percent statistic isn't arbitrary. Pershing and others compared ocean trends and presented the figure to NOAA in April.
Pershing's work illustrates that the Gulf is indeed among the fastest-warming bodies of water, said Roger Griffis, climate change coordinator for NOAA Fisheries Service.
The Gulf of Maine, he said, is "one of the poster children, unfortunately, for major changes."
Its historical chill and strong tidal currents, which mix the waters and increase nutrients, make it one of the most productive marine ecosystems and a key summer territory for rare whales.
But half of 36 fish stocks studied in the Northwest Atlantic Ocean, including many commercial species, have been shifting northward over the past 40 years, a 2009 NOAA report said.
Ironically, the warmer water has created ideal conditions for lobsters and contributed to an overabundance in recent years, causing prices to tumble to their lowest point in nearly two decades in Maine. But warming is on a path to force them to move north or die off, Steneck said.
Puffin chicks have starved and died because of a lack of the herring and hake they need to grow and fledge. Seemingly overnight, longfin squid — normally found in warmer, more southerly waters — appeared, Record said.
Scallops, also an important economic element in the Gulf, are vulnerable to ocean acidification, which scientists say is another effect of increased carbon dioxide in the atmosphere.
The changes threaten a three-state industry valued at more than $1 billion in 2012, a year in which fishermen caught more than 550 million pounds, NOAA statistics say.
Governments are reacting by creating new commercial fisheries; Maine regulators are in the process of creating a licensing process for black sea bass, a species associated more with the mid-Atlantic.