"These changes are very real, and we're seeing them happen quickly," said Malin Pinsky, a biology professor at New Jersey's Rutgers University who studies ocean temperature change and was not involved in the research that resulted in the 99 percent statistic.
It is a rallying point for environmental activists, who see the response to the temperature rise and its impact on fisheries as a touchstone for the global debate about climate change.
"The warming is already here," said Jeff Young, a spokesman for Pew Charitable Trust's oceans project, which has campaigned in favor of restrictions on fishing for herring, another species leaving for colder water. "And we have to deal with it."
The rising waters in the Gulf — a big dent in the East Coast stretching from Massachusetts to Nova Scotia and New Brunswick — have interfered with the work of Diane Cowan, founder of the Lobster Conservancy, who has conducted lobster censuses in New England for 22 years.
The shore of a cove off Maine's Friendship Long Island has long been the best site on the East Coast to find baby lobsters, she said. Around 2007, she couldn't lift a rock without finding one, and usually found several.
But the rising sea has prevented her from getting there much since 2010, she said, because it's almost always underwater.
On a recent August morning, she made it to the site and found 19 young lobsters — far down from the huge colonies she found seven years ago, she said.
"Things have changed dramatically," she said.
The rising sea is connected to the warming waters because higher temperatures make the water less dense, said Bob Steneck, a professor at the University of Maine's School of Marine Sciences.
Until 2004, Gulf temperatures were increasing by about 0.05 degrees per year since 1982, about in line with worldwide trends, said Andy Pershing, chief scientific officer at the Gulf of Maine Research Institute and the man behind the 99 percent figure. But then the pace accelerated to about a half-degree per year — nearly 10 times faster.
Scientists are not certain why. The rest of the oceans are also warming, albeit not as fast, as increased carbon dioxide in the air has contributed to rising temperatures, Pershing said.
"Atmospheric events" could be pushing additional heat into the Gulf, causing a "perfect storm" of conditions that combine to dramatically raise temperatures there, said Nick Record, a research scientist at the Bigelow Laboratory for Ocean Sciences, a Maine center for oceanography. Pershing and many peers agree.
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.