Brookhaven officials said Tuesday they had launched a study to determine possible causes of contamination in the Setauket Harbor watershed that has prevented swimming and shellfishing there.

Town officials said they have hired Cornell Cooperative Extension to begin testing water to find the sources of bacteria in the historic harbor.

"Setauket Harbor and the surrounding watershed are threatened and we must take action now to prevent further contamination," Supervisor Edward P. Romaine said in a statement. "This is just the beginning of our plan. We intend to study our own infrastructure throughout the town to assure that we are doing everything we can to reduce storm-water runoff into our waterways."

The state Department of Environmental Conservation has listed the harbor and nearby Little Bay as "uncertified," meaning shellfishing is banned. The ban also affects part of Conscience Bay.

Excessive sediment also makes both areas difficult for boaters to navigate because it has filled in shallow areas, officials have said.

George Hoffman, a founder of the Setauket Harbor Task Force, a citizens group created last year to advocate cleanup efforts, said he welcomed the town study.

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"What this report's going to do is give us a baseline. It's going to be a really good metric to tell us what we need to do," Hoffman said. "It's going to save us months of work. . . . Our goal is to bring back shellfishing."

Town officials said they have spent millions of dollars to reduce pollutants that enter the harbor through storm drains. In a news release, officials said "every potential point source of pollution from the town's infrastructure will be analyzed and targeted for mitigation if required."

Local residents also will be asked to help by cleaning up after pets, reducing fertilizer on lawns and refraining from dumping chemical wastes in storm drains.

Hoffman said the town effort, if successful, could restore the harbor's role of providing work for local fishermen and recreation for swimmers and boaters.

"Everybody remembers 20 years ago when they were pulling bushels of shellfish out of that harbor," he said. "At one time there were a lot of people making their living from the harbor. . . . We'd like to have that back."