ROCHESTER — The Great Bay Municipal Coalition will hold a meeting Thursday to discuss the local impacts of the proposed actions made by the state Department of Environmental Services and the federal Environmental Protection Agency, including the permit distributed to Newmarket last month.

The coalition, comprised of Dover, Rochester, Portsmouth, Exeter and Newmarket, firmly believes nitrogen levels in the Great Bay estuary can decrease naturally and is not backing down from NHDES or EPA, hoping to prevent communities having to “subject to residual designation that will keep these communities in a permanent state of non-compliance,” according to a public statement.

The battle is over the Great Bay estuary’s current nitrogen levels of between 15 and 20 milligrams per liter. NHDES and EPA are requiring permits to limit the levels of nitrogen to just 3 milligrams per liter, which, according to Dover’s environmental consultant Dean Peschel, will cost the communities within the Great Bay basin more than $1 billion to obtain. Affected communities include, but are not limited to, Rochester, Portsmouth, Exeter, Newmarket, Durham, Madbury, Dover, Lee, Barrington and Nottingham.

In order to limit nitrogen to this level, Dave Cedarholm, Durham’s town engineer, said it would require using a carbon source such as methanol or ethanol.

“I’d rather put that in my car than a wastewater treatment plant,” he said.

The coalition recently filed a motion for reconsideration in a decision in a court case over nitrogen levels from earlier in November. A judge’s recent ruling declined to determine if the NHDES was required to follow the New Hampshire Administrative Rulemaking procedures in developing and imposing nutrient criteria for the Great Bay Estuary. The court decided this is a federal issue and that the EPA is the organization that would make the ultimate decision to harm the coalition and force those communities to pay for costly updates to their water treatment facilities.

Durham has been successful at limiting its nitrogen levels to below 5 milligrams per liter in the summer, but it is nearly impossible to get levels that low during other parts of the year due to the number of college students in town. One of the biggest reasons for high nitrogen levels, according to Cedarholm, is urine.

“The spikes in nitrogen that we see is from urine,” Cedarholm said. “We have done studies that show that on Thursdays, Fridays and Saturdays, when college students are drinking beer, there is a spike in nitrogen.”

While Cedarholm blames urine, something the community cannot avoid, Peschel has graphs of studies that prove the increased nitrogen level that raised recent concerns for the system in the region from 2005 to 2008 are from heavy precipitation. Since 2008, the levels in the estuary have dropped back to levels seen before 1980.

“The nitrogen reduction requirements being imposed are based on fundamentally flawed analysis and obviously incorrect ‘scientific’ conclusions,” Peschel wrote in a public statement. “DES representatives admitted under oath that the tidal river data confirm nitrogen control will not materially improve water clarity because it is not a nitrogen induced problem — it is natural.”

Dover received professional help earlier this year from Wright-Pierce Engineering, which designed a plan to decrease the city’s nitrogen discharge from its current operating level to 8 milligrams per liter.

Wright-Pierce said this level would address the troubled health of the estuary and that 3 milligrams per liter is not necessary.

“Imposition of these erroneous regulatory mandates will likely bankrupt small communities throughout the watershed and misdirect local resources on an unprecedented scale,” Peschel wrote. “Residual designation will cede land use control to EPA. Environmental requirements and land use regulations developed by environmental groups and dictated by Federal and State Regulatory agencies will be our future.”

The communities affected will receive their permits within the next two years. The EPA issued a final National Pollution Discharge Elimination System permit to Newmarket on Nov. 16, which calls for nitrogen levels to be decreased to 3 milligrams per liter, which will be tested in a rolling seasonal average.

The EPA stated in a public statement that “a nitrogen limit of 3.0 mg/L is as stringent as necessary to ensure compliance with applicable water quality standards, including New Hampshire’s narrative nutrient criterion.”

This permit, according to Peschel in a public statement, would be profound on affecting future generations in the area. Cedarholm said this information, however, is premature.

“We don’t have data to show too much yet,” Cedarholm said. “It’s too early.”

Cedarholm does believe, though, that within the next 20 years, the communities surrounding the Great Bay basin will be seeing significant changes and will have to spend a large amount of money to comply.

“EPA has acknowledged that at least 60% reduction in ‘nonpoint’ (i.e., septic system, lawn and farm runoff, golf courses, school athletic fields, etc.) will be required while acknowledging that this reduction is not physically attainable,” Peschel wrote, adding that NHDES and EPA plan on requiring treatment systems to be placed on each septic tank owner or “skewering areas” with septic tanks and building centralized treatment, which will cost families at least $15,000.

“This must be stopped now,” Peschel wrote.

The meeting will be held on Thursday at 7 p.m. in the Rochester City Hall Opera House at 31 Wakefield Street.