THE HEALEY ADMINISTRATION issued final regulations on Wednesday aimed at addressing Cape Cop’s nitrogen pollution, which is caused by wastewater from septic systems finding its way into waterbodies where it spurs the growth of algae that chokes off plant and wildlife and often leaves a foul smell.

The new regulations allow towns to apply for watershed permits that would spell out how a municipality would reduce nitrogen output to safe levels over a 20-year period. The permits would allow the construction of centralized sewer systems, as well as alternative approaches such as aquaculture, permeable barrier walls, and fertilizer reduction.

If towns do not apply for watershed permits within two years, their residents would be required to upgrade their individual septic systems within five years at a cost of $25,000 to $35,000.

Many Cape Cod communities have been trying to address nitrogen pollution for years, and some are farther along than others. Orleans, Chatham, Harwich, and Brewster developed a watershed permit to clean up Pleasant Bay using a combination of sewers, permeable barriers, and aquaculture. Falmouth, which has 14 estuaries in need of nitrogen relief, has a lot more work to do.

On The Codcast in January, officials from Orleans and Falmouth were both eager to address nitrogen pollution. Both ruled out the house-by-house approach as unworkable and too expensive, but the Falmouth official, Stephen Rafferty, was also wary of the cost associated with the town-wide permitting process. He said the Department of Environmental Protection devised its either-or approach to avoid creating an unfunded mandate that the state would have been required to address with funding.

The draft regulations issued last October gave the Department of Environmental Protection the power to designate parts of Martha’s Vineyard, Nantucket, and southeastern Massachusetts as “nitrogen sensitive areas.” That provision was dropped from the final regulations after residents from those areas complained that they didn’t have as much time as their counterparts on the Cape to investigate nitrogen pollution and its causes.

The Department of Environmental Protection cited a number of possible sources for funds to address nitrogen pollution, including the Massachusetts Clean Water Trust, the Cape and Island Water Protection Fund (supported by a tax on lodging and short-term rentals), and Barnstable County’s Aquifund.

Healey’s tax plan, which she filed earlier this year, increased tax rebates for septic system upgrades from $6,000 to $12,000. The Senate, in its tax plan, proposed a top rebate of $18,000. House and Senate members are currently reviewing the tax plans of the two branches to find common ground.

The Conservation Law Foundation sued the Department of Environmental Protection in 2021 to force the cleanup of nitrogen pollution on the Cape. The foundation put its lawsuit on hold in 2022 after receiving assurances it would overall existing septic and wastewater regulation.

Maggie Nivison, an attorney at the foundation, hailed the issuance of the final regulations. “Toxic algae outbreaks destroy our waters, sicken people, and threaten the Cape’s critical tourism economy. The state has finally taken this crisis seriously, and these new rules are a tremendous first step in finally combatting this pervasive problem,” she said in a statement.