Southampton Town officials say boring an opening in a barrier island off Hampton Bays could help reverse years of ecological decline in a murky and stagnant swath of Shinnecock Bay.

Installing the opening, composed of one or more steel and concrete tunnels under Dune Road, could cost $20 million to $30 million, Supervisor Jay Schneiderman said. It would include a floodgate to shut the opening during storms that would be the first of its kind on Long Island.

Schneiderman has taken early steps in studying the project, which he said would introduce cold and clean ocean currents to a part of the bay where nitrogen-rich water stagnates for weeks, contributing to algal blooms that have poisoned shellfish and wiped out eelgrass beds.

“It’s like flushing a toilet,” he said.

Schneiderman, who took office a month ago, said he has had early talks with a state Department of Environmental Conservation official about funding the project using superstorm Sandy aid earmarked for coastal protection on Long Island.

While eastern Shinnecock Bay benefits from flushing via the Shinnecock Inlet, water stagnates in a western portion that includes Tiana Bay, said Stony Brook University marine biologist Christopher Gobler. The area had outbreaks last summer of rust tide and brown tide algae, shellfish poisoning and low oxygen levels.

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“The farther you go to the west, the worse the water quality gets,” said Gobler, who heads the university’s Shinnecock Bay Restoration Program.

Long Island’s southern bays have declined since the 1980s because of algal blooms fed by nitrogen pollution from household septic systems, but flushing the bays with ocean water has proved helpful.

Stony Brook researchers have seen clearer water in part of the Great South Bay since a breach carved by Sandy in 2012 reconnected the area to the ocean near Bellport.

But, Gobler cautioned, the flushing effects of the ocean can be unpredictable. An inlet may have marked benefits in one swath of a bay but leave nearby areas unimproved.

“The theoretical basis for this is spot-on,” Gobler said of the floodgate concept. “When you start getting to the reality of it, it’s less clear how it would move forward. It would have to be thought out really carefully.”

Janice Landis, president of the Hampton Bays Civic Association, said the group has sought ways to restore the western bay.

“The water, besides being beautiful, it’s the economic engine of the community, and the quality of it has become so jeopardized that it’s beyond comprehension,” she said.

Southampton Town Councilman John Bouvier, an engineer who has worked on the floodgate idea, said it could provide quick relief to the bay while officials work on longer-term solutions to nitrogen pollution, such as high-tech systems that filter nitrogen from waste.

“We’re looking at a 20- to 30-year potential problem to solve,” he said. “But in the meantime, there are other things we can do.”