The Wampanoag Tribe of Gay Head (Aquinnah) has agreed to lease its shellfish hatchery on the shore of Menemsha Pond to the Martha’s Vineyard/Dukes County Fishermen’s Association for $100 to raise winter flounder. The partnership is part of a federally funded two-year $308,000 National Sea Grant project to find ways to restore one of the most troubled fish resources in Southern New England.

For more than a year scientists from the University of New Hampshire together with local scientists have been out surveying the waters of Menemsha Pond and Lagoon Pond collecting data and samples, as part of the project. The first phase involved water sampling of the two ponds.

The effort now shifts to the second and perhaps most important part of the effort, raising 50,000 juvenile winter flounder in the hatchery to be released later next year into the two ponds. Work has already begun to get the hatchery ready.

Elizabeth Fairchild, the lead scientist, a professor at the University of New Hampshire, said she is pleased by the 13-month partnership and appreciative of the efforts of many Vineyarders to make it a success. Having a place to raise the baby winter flounder, tied to one of the ponds being studied, is key to the success of the project, she said.

The building hasn’t run as a hatchery since before 2006. Two saltwater pumps at the facility were destroyed when the building was hit by lightning in that year. But it has already been used for the raising of quahaugs, bay scallops and oysters. And there is already plenty of information about the health of Menemsha Pond from work done in federally funded bay scallop restoration work by the tribe.

“I am truly pleased and proud that the Tribe; through the efforts of our Natural Resources Department can once again assist the surrounding community in these types of initiatives,” said Cheryl Andrews-Maltais, chairman of the tribe. “This partnership is good fit to bring together our collective resources and skills. We look forward to the success of this program, and we hope to continue to work together on this and other projects of mutual benefit to all of us as Island residents.”

Warren Doty, president of the Martha’s Vineyard/Dukes County Fishermen’s Association, said the grant provides for enough funds to retrofit the facility to raise fish. As much as $20,000 from the grant will be used to replace the pumps and get the place working. Mr. Doty and Brett Stearns, director of the tribe’s Natural Resource department, met on Wednesday to look over the facility together. Mr. Doty said the help of the tribe is a huge contribution to a traditionally abundant resource in these waters. “The water flow is right. They’ll be getting water straight from Menemsha Pond, it couldn’t be better.”

Winter flounder were so named because they migrated each winter into shallower water where they were more readily found and caught.

Also called “black back flounder,” they were among the most abundant fish in southeastern Massachusetts not many years ago. Today, Mr. Doty said: “Winter flounder are the most depleted groundfish stock.” The state has established a 12-inch minimum size and a 50-pound minimum trip limit in Southern New England. The state recreational limit is 12-inch minimum size, two fish bag limit, and fish can only be landed from April 23 to May 22; and from Sept. 24 to Oct. 23.

“The federal government limit for fishermen is zero.” “Winter flounder is the most restricted groundfish,” Mr. Doty said. The water samplers for the project did find some juvenile winter flounder still in these waters — but very few.

Helping to re-establish winter flounder through a hatchery could have a far-reaching positive result, with the fish returning to these waters as adults in three years. If the locally raised fish can’t be harvested offshore because of regulations; there is a pretty good chance those fish will return if they haven’t been eaten by other fish.

While winter flounder spend most of their adult life in the open ocean, similar to river herring, the fish comes back into coastal waters as fully matured adults to spawn. Those juvenile fish start their life here and go elsewhere.

Unlike other groundfish that are in different levels of trouble, winter flounder are especially at risk. They depend on inshore coastal waters as part of their biological life story. As the water quality and habitat has deteriorated, the fish not only suffered in the past from overfishing offshore, they are in trouble where they spawn.

By stepping in and helping the fish get re-established, the hope is that the animals will flourish.

The first phase of the project involved water sampling in the two ponds twice a month by a team of at least five people in each pond. That work is nearly complete. Ms. Fairchild said the intention was to first establish whether Menemsha Pond and Lagoon Pond were still good winter flounder habitat. Preliminary results from those hundreds of hours of study out in the field and looking under the microscope at the university, point positively ahead.

Ms. Fairchild said she had quite a few undergraduate science students helping to identify animals in the water and in the sediment. Support from the project has come from the Oak Bluffs and Tisbury and Chilmark and Aquinnah shellfish constables, along with a team of spirited citizen scientists.

Mr. Doty, who years ago ran Menemsha Basin Seafood, used to purchase winter flounder and other species of fish, for shipment to the mainland. He recalled when local Menemsha draggermen counted on winter flounder in early spring before the start of the squid season. Small draggers, not much more than 50 feet in length, fished out of Menemsha and harvested thousands of pounds for shipment to the cities.

Mr. Doty said he has memories of fishermen catching 500 pounds a day in places like Hedge Fence and Middle Ground. Georges Bank, once the nation’s most valuable fishing grounds, was teeming with them. Winter flounder were once abundant from the Gulf of St. Lawrence to the Chesapeake Bay.

The biggest challenge ahead may not be raising the fish, but searching for further dollars to continue their study to monitor their success. Mr. Doty said he would like to see the project get federal and state funding to go beyond raising the fish and releasing them. He said he’d like to be able to do science on how many of those fish return to these waters and what the implications of their success means farther down the road.

Mr. Stearns and Mr. Doty and Ms. Fairchild are working on a schedule of operation for the next year. Mr. Stearns said they hope to have the sea water running in the hatchery by Thanksgiving. The first step will be raising the food that will be fed to the little animals. He said the second floor of the hatchery which was used to raise algae to feed shellfish will be retrofitted to raise rotifers, a microscopic animal that will be fed to the baby fish. Mr. Stearns said not a lot of effort is required to make the change.

Early next year, Ms. Fairchild said they will go out and harvest adult winter flounder to be used as brood stock for the spawning of baby fish. Well into spring, the hatchery will be a nursery for 50,000 tiny fish. They’ll be released into the two ponds later in the year to get them genetically tagged so they’ll return to these waters as adults in three years.