Brookhaven has adopted a law requiring upgraded sewage treatment systems near lakes and rivers to reduce the flow of harmful nitrogen into waterways.

The law, aimed at protecting fragile bodies of water such as Setauket Harbor and the Carmans River, was approved unanimously by the town board on Thursday. The vote came two days after Suffolk County Executive Steve Bellone dropped a planned referendum to impose a water fee for sewage treatment expansion and environmental protection.

“We’ve all watched our waters degrade. . . . Part of the problem is nitrogen,” Brookhaven Supervisor Edward P. Romaine said after the town board vote. “We cannot continue to pollute our waterways.”

The town law will create “nitrogen protection zones” within 500 feet of waterways. New houses in those zones will be required to install upgraded sewage treatment systems.

Supporters said the law could help fragile waterways start to recover after decades of pollution from nitrogen caused by untreated sewage.

Brookhaven officials said the law would have more stringent requirements than county laws for sewage treatment systems.

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The town law requires systems to emit no more than 8 milligrams of effluent per liter of water, Romaine said. County law allows no more than about 19 milligrams per liter.

The law received support before the vote from the Affiliated Brookhaven Civic Organization, the Setauket Harbor Task Force, and Kevin McAllister, president of the Sag Harbor-based environmental group Defend H2O.

“I ask you, seize the day,” McAllister said.

“It’s timely, it’s needed and I’m glad you’re moving forward with it,” George Hoffman, of the Setauket Harbor Task Force, told town board members.

McAllister and Hoffman both noted Bellone’s decision to temporarily scrap the proposed referendum, which faced skepticism from state lawmakers who would have to approve placing the measure on the November ballot. State officials said they worried money from the water quality program would be used for other purposes.

County officials said they will try again next year to place the referendum on the ballot.

The Brookhaven law contains a waiver provision for homes affected by natural disasters such as hurricanes, Romaine said. Some board members had expressed concern that homeowners repairing storm-damaged houses may be required to install sewage treatment systems they cannot afford.

The price of home-based septic systems can range from $10,000 to $25,000.

Romaine said the “act of God” provision in the law allows for the septic system requirement to be “waived due to a financial hardship.”