The Environmental Protection Agency has finalized a new permit for a dozen communities around Great Bay, capping a years-long effort to control nitrogen pollution in the protected estuary.
The five-year permit takes an unusual approach to setting limits for each municipality’s output of nitrogen – a nutrient that’s overloading the bay, causing eel grass to die and severely degrading the ecosystem.
All 12 towns, comprising 13 wastewater sources, are covered by this single permit. It doesn’t stipulate exactly how they should meet the new goals – whether through upgrading their wastewater treatment plants, or other voluntary methods.
“Given that … any delay could mean the difference between potential recovery or collapse of the ecosystem, EPA opted for a precautionary, adaptive approach because it will allow for more expeditious application of nitrogen reductions,” the agency wrote in its response to stakeholder comments.
“EPA concluded there is urgency to regulate nitrogen in order to prevent further degradation since total nitrogen load is population driven and the Great Bay estuary watershed population is and has been fast growing,” the agency says.
The EPA says stakeholder comments on their draft of this permit pointed them toward an opt-in rather than opt-out approach -- one that some advocates say is less strict than what the agency initially proposed.
The EPA says data shows nitrogen sources including stormwater and septic runoff are now a bigger concern in Great Bay than the wastewater plants, many of which have been upgraded in recent years.
Ideally, the EPA says, towns would reduce nitrogen from those “nonpoint” sources by about 45% – but the state, not the EPA, is the permitting authority on those issues. New Hampshire is one of only a few states that defer any stormwater permitting to the federal government.
“The effectiveness of the [permit] rests on the strength of EPA’s assumption that nonpoint source and stormwater point source reductions will in fact be voluntarily undertaken by participating municipalities,” the EPA wrote in its response to stakeholder comments.

“Therefore, if such reductions do not occur and water quality standards are not achieved, EPA will be forced to seek additional reductions in the future, likely resulting in more stringent load limits at the [wastewater treatment plants]," the EPA says.
In theory, the agency says the permit shouldn’t have to lead to major short-term costs for most towns to upgrade their sewage plants. The potential exception is the city of Rochester, which was a lead opponent of much of this plan.
The final permit includes some key changes from the earlier draft. It drops one required monitoring plan and adds a provision that lets towns seek higher nitrogen limits if they expand their sewer systems.
The final permit also underscores voluntary options for towns to meet their nitrogen goals, and makes those goals seasonal, rather than annual -- which could make them easier to meet, according to Great Bay-Piscataqua Waterkeeper Melissa Paly.
Paly, who works with the nonprofit Conservation Law Foundation, says she's glad the final permit recognizes the severity of the estuary's nitrogen problems. But she worries that it "lacks a clear roadmap" for municipalities to make the necessary cuts.
“We support the flexibility that this permit approach gives municipalities, but are concerned about the lack of structure and accountability in how they would achieve significant stormwater and nonpoint source controls in the five-year timeframe of this permit cycle," Paly says.
She says she hopes the state will now take the lead on creating options to help towns get there.
Regardless, the EPA says it may want to fall back on more traditional, town-by-town nitrogen limits for Great Bay communities in the event that this more flexible permitting approach doesn’t yield results quickly – or even if stakeholders appeal the new permit, in what could turn into a lengthy court battle on top of an already years-long effort to restore the estuary.
This story has been updated with more details and stakeholder comments.