The state has awarded nearly $1 million in grants to Brookhaven Town for marina pump-out facilities and other water quality improvement projects.

The projects, which include studies of storm-water outfall pipes and construction of ladders to help fish and eels move upstream, are designed to reduce the flow of pollutants in bays and harbors, as well as restore traditional river habitats.

Brookhaven Supervisor Edward P. Romaine said the new pump-out stations in Patchogue and Port Jefferson, and an expanded station in Mount Sinai, would augment a fleet of town boats that offer pumping services to boaters.

“This is crucial,” he said Monday. “This money will ensure that waste doesn’t go in our harbors and waterways.”

The grants, from the state Regional Economic Development Council, are worth a total of $921,000 and include:

$388,500 for new pump-out facilities intended to help cut wastewater from being dumped by boaters into North Shore harbors and Great South Bay.

$345,000 for a “fish ladder” on Swan River in East Patchogue. Town officials said the ladder will help restore river herring to the upper Swan River and ease access to habitat for eels and brook trout.

$187,500 to create an inventory of outfall pipes and determine which are most responsible for pollutants in local waters.

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The initiatives were hailed by other local officials and environmentalists.

Patchogue Mayor Paul Pontieri said a new pump-out station would augment the town boat that provides pumping services to boaters on Great South Bay and the Patchogue River.

“I think it’s critical to the health of the rivers. It’s critical to the health of the bay,” Pontieri said Monday. “If people have a pumping station that people can go to, that would be great.”

Port Jefferson Mayor Margot J. Garant said a village consultant has found high levels of pollutants in Port Jefferson Harbor, and she said village officials worry that some boaters are not using the town pump-out boat.

George Hoffman, of the Setauket Harbor Task Force, said the state grants are “good news” and should help local efforts to clean up waterways that are polluted by stormwater runoff containing pesticides and untreated sewage from cesspools.

“We have to find a way to stop the stormwater from getting in the harbor, because that seems to be the number one reason for the problems,” Hoffman said.

He added a new pump-out station would help owners of the 100 boats moored in Setauket Harbor, who must go about 20 minutes to the nearest pump-out station in Port Jefferson.

“For someone in Setauket Harbor, they really have to go out of their way to find a pump,” Hoffman said.