State and local officials are developing a multimillion-dollar plan to tackle the problem of excess nitrogen in Long Island’s waterways, establishing recommended limits on the nutrient and identifying areas best suited for sewers or other wastewater upgrades.

The Long Island Nitrogen Action Plan, funded with $5 million in the current state budget, is spearheaded by the Long Island Regional Planning Council and the state Department of Environmental Conservation.

The two groups held three meetings — two in Suffolk and one in Nassau — over three days last week, soliciting public comment on the draft scope of the plan.

The overall process outlined in the plan covers four years, Jim Tierney, the DEC’s assistant commissioner for water resources, said at Tuesday’s meeting in Riverhead, which attracted a standing-room-only crowd. “It’s an ambitious plan,” he said.

The plan has two phases, beginning with an “early-action” element, designed to gather existing data on the current nitrogen problem.

Excess nitrogen — coming from septic systems and cesspools, fertilizer runoff and other sources — has caused a variety of harmful effects in Long Island’s waterways.

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The nutrient has led to an increase in harmful algal blooms, decreased oxygen, overgrowths of macroalgae such as ulva, and a weakening of the coastal marshlands that serve as a buffer against harsh wave action during storm events.

The plan also includes gathering information on the siting of wastewater-treatment plants, and a geographic inventory of areas with sewers on the Island, culminating in the creation of a map-based website.

A wastewater map and priority areas in need of advanced wastewater treatment will be identified will be developed for each watershed included in the plan: the areas along the Long Island Sound, the Peconic Estuary Complex, the Western South Shore Estuary Reserve, the Middle and Eastern South Shore Estuary Reserve and another category of waters, which includes Mecox Bay.

Nitrogen-reduction targets also will be developed for each watershed, to be refined in later years. Officials expect the document to provide a science-based tool for guiding future policy around nitrogen reduction.

“The plan is to lean on the science that has been done and select a comprehensive set of indicators as a set of water quality and ecological goals,” according to the document.

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The second phase of the plan includes finding ways to fund some of the plan’s elements.

“The nitrogen problem on Long Island continues to exacerbate,” John Cameron, chair of the Long Island Regional Planning Council, said at the Riverhead meeting. “The challenge is going to be, how are we going to pay to address it?”

The three public meetings attracted government officials, advocates and members of the public, many lauding the effort while also offering suggestions about the process.

“We really like the watershed approach,” Carl LoBue, senior marine scientist with The Nature Conservancy, said at the meeting in Hempstead on Wednesday.

Adrienne Esposito, executive director of Citizens Campaign for the Environment, suggested at that meeting the creation of an “action index” to measure yearly progress of the plan.

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“So we can do a checkup once a year and see how we’re doing,” she said.

The draft scope plan can be found on the DEC’s website at www.dec.ny.gov/lands/103654.html. Written comments will be accepted until Feb. 19 at liwaterquality@dec.ny.gov