FREEPORT — Clammer Clint Goodenow motored his skiff up to a small, white buoy in the Harraseeket River Monday afternoon and began pulling up yards of rope from the bay floor below.

After reaching the end of the rope, he leaned over the side of the boat and plunged his hands into the water, grabbing hold of a black metal trap. In what appeared to be a delicate balance, Goodenow heaved the trap into the small boat, positioned it above a gray rectangular storage container, and flipped open the latch at the bottom.

Dozens of European green crabs crashed into the container — some one or two inches across, others five or six. He then pounded the top and sides of the trap to knock loose the remaining crabs.

Three traps later, the 100-pound container was brimming with crabs. Some attempted to spring loose, but were quickly snatched up and shut in with a lid.

Goodenow, who is part of the largest effort in the state’s history to study the decline of shellfish populations, describes the swarms of crabs he has seen in the last few years like something from a horror movie.

“They just boil out of the water,” he said.

In recent years, clammers say the rapid growth of the green crabs along sections of Maine’s coast has ravaged shellfish populations, particularly mussels and soft-shell clams.

There is concern now that even Maine’s lobster industry may be at risk.

The crabs, previously held at bay by long, cold winters, have swelled in numbers in the past couple decades due to rising water temperatures that no longer keep their populations in check.

The Freeport-funded project now has more than a month of work under its belt, stewarded by town clammers and lobstermen at the direction of scientists. And while the project has a focus on green crabs, it will also gather and analyze data on the impact of other factors believed to be contributing to the decline of clam populations: ocean acidification, which dissolves clam shells, and disease.

Researchers and fishermen hope the study can find an effective method to reduce the impact of the crab infestation. If they don’t, they believe it could spell the end of the state’s $25 million fishery and be disastrous for the coast’s ecosystem.

“We’ve been so spoiled in the past and didn’t do anything,” said Chad Coffin, president of Maine Clammers Association, noting that he first noticed green crabs in 2007. “That’s when I first started piecing it together, but I didn’t understand how bad it really is.”

Freeport Town Manager Peter Joseph said clammers working on the project, which involves not only trapping, but fencing off of certain areas, are hauling in about 400 pounds of crabs every three days.

He said the town hopes the nearly $70,000 study will shed light on how to deter green crabs in a way that can be replicated by other towns.

“All marine resources are connected out there, so what benefits us, benefits everybody,” Joseph said.

Kohl Kanwit, public health bureau director for the Department of Natural Resources, said while the disappearance of clams could be caused by a number of factors, green crabs in Casco Bay pose a “huge problem.”

In a recent tour of Freeport’s tidal flats with Coffin and state biologist Pete Thayer, Kanwit said the crab invasion seems to have reached a new level.

“It was shocking to see the numbers of crabs at low tide up under the marsh, burrowed up under the grass,” she said, referring to the salt grass that lines much of the Harraseeket River. “It’s unbelievable how many are there.”

Kanwit said in recent years clam predators like green crabs and the moon snail have completely shut down commercial harvesting in the once productive clamming area of Northern Bay in Penobscot.

“(Penobscot clammers) tried to resolve their problems by removing the moon snails and they were fairly successful with that, until green crabs moved in,” she said. “The entire flat has no clams anymore, at least not anything anyone can commercially dig.”

Although the crabs are known for eating the juvenile clams, also known as spat, Kanwit said she found “fairly large clams” at entrances to the Freeport flats with chips taken out of their edges, suggesting that some crabs have moved on to larger prey.

Right now, the crabs’ favorite meals are clams, but Coffin warns other species, including the Maine’s most sacred seafood, may be at risk.

“(The crabs) food preference has systematically moved through all of shellfish resources on a sequence based on convenience,” he said, noting that predation has killed off most of the scallops and mussels, and has now moved onto clams. “When the clams are gone, what are they going to eat? People may think lobsters are big and tough, but they’re not.”

Kanwit said in lab tests pitting lobsters against green crabs, the crabs have dominated. They don’t have evidence of this phenomenon in the wild yet, she said, but lobstermen are reporting catching green crabs in deeper water than they have ever seen.

“It’s potentially logical that it might be happening,” Kanwit said of green crabs preying on lobsters. “It’s hard to make the assumption at this point.”

Richard Wahle, a University of Maine professor who studies marine life in New England, said finding the crabs in deeper water is a disturbing development.

“We’ve always sort of dismissed green crabs interacting with lobsters because they have pretty much disappeared at a 25-foot depth along coastal Maine,” he said. “Seeing green crabs in deeper water does open the possibility of green crabs interacting more with lobsters. That’s something to be concerned about.”

Another alarming result of the green crab invasion is the erosion of salt grass, an important stabilizing plant, along the river banks, said Brian Beal, a professor at the University of Maine at Machias and lead researcher of the Freeport project.

“The salt grass dying. There’s maybe two or three feet of dead sod,” he said. “It’s getting ravaged.”

Beal, who has studied green crabs since the 1980s, said the only evidence he’s seen of this kind of erosion is in a photo from the 1950s that hangs on his office wall. A marine warden stands in the marsh with hatchet he used to chop away the dead sod that had been eroded by the crabs.

Back then, water temperatures soared, creating a fertile environment that fostered a surge of green crabs eerily similar to the one today. The crabs devastated clam populations until a severe cold snap settled in during the 1960s, effectively killing them off and allowing shellfish to return.

The concern now is that extreme increase in water temperatures is not part of cyclical process, but an unnatural phenomenon, said Wahle, who published a paper in late June about water temperature’s impact on lobsters.

One of the most serious threats thought to be caused by the warming temperatures is shell disease, he said, noting that in the last few years they’ve seen a ten-fold increase in parts of Maine.

And while relatively long-term impacts of climate change can seem abstract, Coffin, who has been ringing the alarm about green crabs for several years, said their impact as a result of a changing climate is something that can be seen immediately.

Now, he said, clammers and lobstermen in other towns, who at first dismissed the problem, are beginning to pay attention.

“The full effect could take 20 years,” Coffin said. “But it’s going to happen unless we can do something and start fighting back.”

Will Graff can be reached at 781-3661 ext. 123 or wgraff@theforecaster.net. Follow him on Twitter: @W_C_Graff.