The final phase of Northport’s massive wastewater treatment plant overhaul started this month after a yearlong delay, with workers starting to replace two critical sections of the village’s fragile, Depression-era sewer lines.

The multiyear project is projected to cost $13.3 million once complete, but with $11.9 million in state and county grants and strategic financing, village officials said residents will pay a fraction of the cost — about $1.4 million, or 10.5 percent.

“The state of these two [sewer] mains is really the rationale for why the state has given us money” for this phase, Deputy Mayor Henry Tobin said.

Village officials have spent $700,000 from reserves on the project, leaving less than $694,000 unpaid and uncovered by grants, he said. The village is still applying for new grants to cover remaining costs.

The third and last phase, which was delayed when workers found obstructions and other problems underground, is projected to cost $6.25 million. It will replace two deteriorated sewer lines.

The project, which began in 2013, is part of a mandate from a 2003 agreement between New York, Connecticut and the U.S. Environmental Protection Agency to improve water quality in the Long Island Sound region. It requires Northport to cut the sewer treatment plant’s nitrogen output to 10 pounds or less per day — compared to its 2012 levels of 21 pounds per day, Tobin said.

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The village currently has an average nitrogen output of 5 pounds or less per day, said Damon McMullen, Northport trustee and commissioner of wastewater treatment. In the first two project phases, the village upgraded its sewer treatment plant at Scudder Beach, relined sewer mains and rehabilitated manhole covers to prevent groundwater and storm water entering the sewer system.

The two 8-inch-diameter lines being replaced in the current work phase run beneath Woodbine Avenue and along the Northport Harbor shoreline, where pipes and a pump station are submerged at high tide and exposed at low tide. One 12-inch-diameter pipeline made of high-density polyethylene will replace both. It will be tunneled underneath the sand and run parallel to Woodbine, between Fifth Avenue and Beach Avenue.

The village also received a loan of up to $9 million through the state Environmental Facilities Corporation, which made it possible to pay for work while waiting for grant money.

The village has only spent $6.2 million of the loan so far, and reimbursed $4.4 million of that through grants, leaving $1.8 million to be repaid when promised grants are received.

The corporation also announced it would provide up to $4 million more for the project, with any money the village uses split: 25 percent in grants and the rest in a low-interest loan.

Later this year, village officials are to decide how to finance the remaining $694,000 in projected debt. Tobin said options include bonding, seeking an extension from the corporation, raising taxes, or some combination of all three.