Maine officials have begun a program to reopen some of the tens of thousands of acres of clam flats that are closed to harvesting because of poor water quality.

The shellfish growing area team at the Department of Marine Resources is taking a close look at flats that have been closed because of high bacteria levels. By working with town officials and focusing on specific areas, the team hopes to reopen some of the flats to harvesting and make them productive.

Clam digger Chad Coffin of Freeport calls the new unit a “shellfish SWAT team.” The effort will go a long way toward helping Maine’s clam industry and its nearly 1,800 licensed diggers, he said.

“To see them come up with the shellfish SWAT team is a breath of fresh air,” Coffin said. “Everyone’s excited about it.”

More than 140,000 acres of shellfish growing areas were closed to harvesting in 2007, according to the department’s most recent statistics. An additional 36,000 acres were restricted or conditionally closed depending on weather or seasons.

Besides soft-shell clams, the flats are harvested for smaller amounts of mussels, quahog clams and oysters.

The idea behind the new program is to take a focused look at closed areas — some of which have been shut down for years — and work with local officials to get some of them back open, said Linda Mercer, director of the department’s Bureau of Resource Management. They include the Harraseeket River in Freeport, parts of Maquoit Bay off Brunswick, the Medomak River in Waldoboro and numerous small coves and inlets.

Most of the targeted areas have been closed because of water quality issues caused by faulty septic systems, runoff and the like. The water quality can be improved by conducting shoreland surveys, analyzing historical water quality data and identifying pollution sources with help from local officials, Mercer said.

“The whole idea is to take a more in-depth look along the coast,” she said. “We plan for this to become an ongoing process.”

Diggers last year harvested nearly 9.3 million pounds of soft-shell clams, valued at $11.7 million. Excluding farmed salmon, that makes clams Maine’s third-most valuable commercial fishery, behind lobster and shrimp.