The survey has tracked 130 species in the bay, although the new analysis focuses on the 25 most common ones.
The data show that most of the changes occurred slowly.
But an abrupt shift showed up in the early 1980s, when bottom-swimming species such as winter flounder and silver hake declined and shallow-water species such as butterfish and bluefish increased.
Microscopic plant-like organisms known as phytoplankton have also taken a nosedive in the deeper waters of the bay, resulting in a decline in the system's chlorophyll levels, the survey shows.
The study authors suggest that zooplankton—free-floating invertebrates that range in size from tiny protozoa to jellyfish—might be gobbling up phytoplankton in shallower waters.
Less of the tiny plants therefore reach deeper levels to sustain bottom-dwelling fish, they propose.
"It's a rerouting of [productivity] from the bottom to the top," Collie said.
Of the animals that still live at the bottom of the bay, a much higher proportion is made up of invertebrates, which Collie believes moved in to fill the void left by fish.
Although the shifts in species composition correlate with the winter North Atlantic Oscillation index—a natural cycle of climate variability—the authors say that global warming is the major driver.
The survey shows that sea-surface temperature in the area of the trawls has increased by 3.6 degrees Fahrenheit (2 degrees Celsius) since 1959.
The URI team presents its findings in the July issue of the Canadian Journal of Fisheries and Aquatic Sciences.
The results of the study agree with what fishers have already been seeing and what diners in the region have been tasting, the study authors say.
Fisheries have switched target catches, so "we are eating more calamari and less flounder," Collie said.
His team predicts species composition in Narragansett Bay will soon resemble estuaries to the south such as Delaware Bay and Chesapeake Bay.
But Nils Stolpe, communications manager for the Garden State Seafood Association in New Jersey, argues that people's seafood diets change for reasons apart from availability.
"The reason we're getting more calamari is because we're getting more sophisticated as seafood eaters," he said.
"Ten, fifteen years ago nobody ate salmon, because we weren't in tune with eating salmon. Now everyone's growing it, and we're a lot more familiar with it."
Stolpe hesitated to apply the study results out of Narragansett Bay to the oceans at large, but, he said, "by the same token, the fisheries are changing. We're seeing more warm-water species farther north than we were 10 years ago, 15 years ago.
"They're catching Atlanta croaker off of New Jersey now, which they hadn't done for 20, 30 years."
According to study author Collie, the results add to evidence suggesting that distributions of marine fish will migrate toward the Poles if they can.
"Obviously, fish in lakes can't migrate," he said. "But there are also subpopulations of marine fish that are adapted to particular spawning locations, such as winter flounder in Narragansett Bay, which may die out."
Still, Collie thinks the new research isn't signaling a death knell for ocean systems.
"The productivity of the ecosystem will continue," he said.
"The worst-case scenario is the whole functioning of the system is collapsing. We haven't seen that yet, but we're looking."