Northport officials are launching a two-pronged initiative to address chronic flooding in the village while capturing and cleaning storm-water runoff before it carries pollutants into the harbor.

Village officials hired Melville-based environmental planning firm Nelson, Pope & Voorhis to study the terrain and develop a comprehensive plan to address both problems on Main Street — and, eventually, the rest of the village.

The goal is to construct different types of small, low-cost projects around the village, each chosen and strategically placed to yield the most significant improvement.

“It’s a lot of small projects that will make a very large impact,” trustee Ian Milligan said.

Phase one is already underway: Last month, the firm began work on a $20,000 hydrology study. Officials said it will take about two months to analyze village topography, water flow and rainfall patterns.

The firm will produce a map identifying where water issues are most problematic.

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“We are going to be looking at the volume of [flood] water,” said Rusty Schmidt, a landscaping ecologist at Nelson, Pope & Voorhis. “But we also will be looking at the pollutants [in storm water runoff]. Nitrogen especially, and bacteria, because those are the two things that affect the harbor.”

In phase two, the firm will develop a report with specific project recommendations and priorities.

The report, which will cost $10,000 and is slated to be completed by the end of the year, will create a long-term road map for flood and storm water mitigation villagewide. But officials said the initial focus will be Main Street, which has long been plagued by flooding during heavy rains. The surrounding hills funnel water runoff directly onto the street and into the bay — along with any pollutants picked up along the way.

Nelson, Pope & Voorhis plans to recommend several solutions for the village, including rain gardens — a concept popular among village trustees for their low cost (ranging from $250 to $5,000) and simplicity.

The gardens are a natural landscaping method that captures storm water in shallow, plant-filled basins and then filters nitrogen, phosphorous and other harmful pollutants through the soil.

Other projects or methods will include the addition of more recharge and catch basins around the village. Recharge basins capture rainwater and lets it soak into the ground, while catch basins collect water and reroute it, typically to recharge basins.

The contractor also will assist with grant applications, a critical step that will help determine how many water projects the village can accomplish in the initial push.

“It’s unlikely that we’re going to be able to put in all the solutions that we want at once,” Milligan said. “We’re probably going to put out a multiyear plan.”

Village Administrator Tim Brojer said Northport officials won’t know the cost, scope and timing of initial construction until they receive the final report.

Deputy Mayor Henry Tobin said the village board has prioritized water-quality issues because Northport Harbor is a fundamental part of the village’s identity.

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“There’s no issue on which we’ve spent more time, thought and money than clean water,” he said. “The harbor is vital to Northport.”

To that end, the village has significantly lowered its nitrogen emissions through a multimillion-dollar overhaul of its wastewater treatment plant.

Now, officials say it’s time to address other sources of pollution, particularly storm water runoff.

“We’ve hit the big targets, the low-hanging fruit,” Milligan said. “A lot of small actions by a lot of different people will be the next phase of water quality improvement.”