Nitrogen and the Great Bay

Public comment period on EPA draft permit ends May 8

A public comment period on a draft nitrogen discharge permit recently issued by the Environmental Protection Agency for Great Bay remains open through May 8, 2020. The draft permit's requirements, if adopted would likely exceed $100 million in Dover alone, and could top $1 billion across all communities in the Great Bay watershed.

Public comments must be submitted by the close of the comment period on May 8 either in hard copy form or electronically to: Michael Cobb (, U.S. EPA, Region 1, 5 Post Office Square, Suite-100 (06-1), Boston, MA 02109-3912.

The City of Dover submitted comments to the EPA on May 6. Dover's comments can be viewed here.

Officials from Dover and throughout the Great Bay region attended a public hearing in February to voice concerns to the EPA about the draft permit.

Dover's City Council recently approved a resolution that urges additional peer review of the draft permit. The Great Bay Total Nitrogen General Permit, or NPDES, will regulate nitrogen levels in the Great Bay watershed, including the levels of nitrogen discharged from wastewater treatment facilities.

The City of Dover has worked for decades to reduce nitrogen in the estuary, investing significantly in science-based wastewater technology and infrastructure.

The City of Dover is calling for a comprehensive and scientific peer review of the EPA’s draft permit prior to issuing the final permit.

City Manager J. Michael Joyal, Jr. said the new draft permit is a change in course from the previous draft permit, focusing now on nitrogen concentration levels for all 13 communities whose wastewater treatment facilities discharge into Great Bay. The new proposed levels and how they will be enforced have raised a number of concerns, including the cost to upgrade the wastewater and stormwater management systems to meet those requirements.

“We have a track record of reducing nitrogen that flows into Great Bay,” Joyal said, adding that city staff and the City Council have made significant wastewater system improvements that help diminish the amount of nitrogen discharged into Great Bay. “That’s the right thing to do for the health of Great Bay. Nevertheless, we have concerns that the levels being proposed in this permit are unnecessarily restrictive and, frankly, unattainable given the science as we know it today. There’s a significant cost in even trying to achieve what would be required by the permit. We’re talking on the scale of hundreds of millions of dollars.”

Following a draft permit issued for Dover by the EPA in 2011, the city has been working with the EPA, the New Hampshire Department of Environmental Services, and other municipalities in the Great Bay estuary to seek options that are less costly and scientifically sound. The Great Bay Municipal Coalition conducted a peer review of the nitrogen criteria cited by the EPA and NHDES and found the data to be unfounded.

Despite concerns and data provided to the EPA and NHDES from Great Bay municipalities, including Dover, the new draft permit calls for a theoretical reduction in nitrogen levels based on outdated studies.

Community Services Director John Storer said the draft permit's proposed yearly nitrogen loading threshold of 100 kilograms per hectare is not based on relevant scientific studies of nitrogen levels and eelgrass growth.

"Experts have dismissed the validity of setting a theoretical loading rate without considering the unique characteristics of the estuary, and have instead recommended that a quantitative, estuary-specific analysis is required to effectively guide watershed management actions," Storer said. "It would be more scientifically objective to focus on actual measured concentration of total nitrogen within the estuary, which is what would directly impact water quality.”

Recent studies show measured total nitrogen concentrations dropping significantly and the eel grass population shows signs of rebounding.

“Our criticism of the theoretical 100 kilograms per hectare loading rate is that it does not consider what the actual nitrogen levels are within the estuary," Storer added. "Our experts suggest targeting a desired end point total nitrogen concentration, and then working to determine what loading rate protects estuary health and eel grass.”

Eel grass was flourishing in the mid-1990’s when nitrogen loading rates were documented in excess of 200 kilograms per hectare, which is more than double what is currently being proposed.

In addition, Storer said “our hope was to receive a permit that allowed for a truly adaptive management program, and one that would foster collaboration for further data collection and analysis to help improve estuary health. But the permit is mandating compliance with something we feel is impossible to achieve, nor is it supported by current science. Unless the permit is modified, it will have significant economic impacts on our community, and will act as growth limiting ordinance.”

At a Feb. 5 City Council workshop, Joyal and Storer reviewed the draft permit with councilors and explained the potential ramifications to taxpayers and water and sewer system ratepayers. The presentation to the City Council can be viewed in its entirety here:

How New EPA Regulations Could Spike Sewer Rates

The Environmental Protection Agency (EPA) is proposing to add nitrogen discharge limits to Dover's wastewater treatment plant permit. If that happens, Dover's sewer rates will increase significantly, depending on the nitrogen limit established in the new permit. The EPA issued a draft permit to Dover in 2013. The draft permit outlines the proposed, additional restrictions. The draft permit can be viewed here.

The City of Dover continues to encourage, support and lead further study of the science upon which the proposed discharge limits are based. To that end, the City of Dover joined with neighboring communities also affected by the proposed discharge limits, forming the Great Bay Municipal Coalition. The coalition consists of the cities of Dover, Portsmouth and Rochester. The coalition aims to ensure the discharge limits are based on sound science, and has raised concerns about the analysis performed by the NH Department of Environmental Services used to establish the “nutrient criteria,” which is the primary document referenced in the EPA mandate to reduce the nitrogen discharge at the Dover wastewater treatment plant to 3 milligrams per liter.

Dover and the Coalition support a workable, alternative approach, which reduces the cost and reduces nitrogen in Great Bay as further study determines the level of reduction needed.

Peer Review

The City of Dover, along with Portsmouth and Rochester, reached an agreement with the New Hampshire Department of Environmental Services in April 2013 to conduct an independent review of the 2009 DES Nutrient Criteria document that largely influenced the EPA’s proposed significant nitrogen discharge limits for wastewater treatment plants. The DES document, “Numeric Nutrient Criteria for Great Bay Estuary”, analyzes available water quality data from the Great Bay estuary, and proposes nitrogen water quality standards for estuary waters.

The peer review is based on questions posed jointly by all three cities, as well as DES. In framing the review, all parties agreed on the scope of work and jointly selected four recognized experts with extensive expertise on estuarine ecology with no conflicts of interest or previous studies of the Great Bay estuary. In addition, public comments were encouraged from other interested parties, including the EPA and the Conservation Law Foundation.

The final report of the peer review panel was issued on Feb. 13, 2014. The complete report can be viewed here.

The Coalition communities are meeting with NHDES representatives in a cooperative effort to determine how best to move forward based on the conclusions presented in the Peer Review Report.

The 2009 DES report that prompted the peer review can be viewed The report can be found here.

The Adaptive Management Plan

The City of Dover continues to support a less costly approach that is nonetheless based on science and still addresses nitrogen reduction in Great Bay. This plan, the Adaptive Management Plan (AMP) limits the nitrogen levels to 8 milligrams per liter; addresses point and nonpoint nitrogen sources; habitat restoration; and monitors progress.

The City Council has voted to support less expensive, alternative measures, including the AMP. In addition, at a goal-setting session on Jan. 28, 2012, and Feb. 1, 2014, the City Council identified this issue as one of its top priorities.

The City of Dover’s environmental projects manager, Dean Peschel, has made several presentations about the AMP and draft permit process, including a workshop session with the City Council in February 2011. 

The original (AMP) presentation materials to the City Council can be viewed here.

A summary of the Adaptive Management Plan proposed by the Great Bay Municipal Coalition can be viewed here.

The Economic Impact of Proposed Nitrogen Limitations

Russ Thibeault of Applied Economic Research, prepared a report that outlines the economic impact of EPA mandated wastewater treatment plant upgrades, compared to the AMP.

Among the report's findings are:

  • The coalition communities alone will have to invest between $74 million and $160 million on their treatment plants to meet the possible nitrogen discharge standards;
  • The coalition communities alone will experience annual incremental costs (debt service and incremental operating costs) of $13 million to $25 million per year (measured in constant 2010 dollars) to meet the possible discharge standards;
  • This annual cost averages about $300-500 per household served by the municipal wastewater treatment systems;
  • This annual cost represents a 50 percent to 100 percent increase in current annual costs per household, measured over the six coalition communities.
  • Measured over the 20 year expected life of the WWTP upgrades, the total economic costs (including principal, interest, operating costs, calculated lost revenues, etc.) are $400-$700 million, and $11,000 to $20,000 per household served;
  • The annual operating and capital costs range from 1.7 percent to 2.1 percent of household income, a significant impact measured by EPA’s economic evaluation standards.

The complete report can be viewed here.

EPA Public Hearing

The EPA held a public hearing on the proposed regulations on Feb. 9 2012, in Dover. 

Congressional Committee Review

Two members of the Congressional Committee on Oversight and Government Reform attended a hearing in Exeter on Monday, June 4, 2012, to hear from communities affected by the Environmental Protection Agency's new, stringent limits on nitrogen levels in Great Bay. Several communities, including Dover, formed a coalition to challenge the EPA's scienctific reasoning for the limits, which could raise sewer rates significantly if enforced.

Committee Chairman U.S. Rep. Darrell Issa, R-Calif., and U.S. Rep. Frank Guinta, R-N.H., attended the hearing, as well as officials from Dover, Exeter, Rochester, Portsmouth and Newmarket. The EPA also provided testimony before the committee.

The City of Dover supports a less expensive, alternative measure, called the Adaptive Management plan, which was created by the Great Bay Municipal Coalition.

The Congressional Committee on Oversight and Government Reform issued a staff memo following the meeting. Among some of the findings outlined in the memo are;

  • “EPA has circumvented the state legislature and violated a number of standard processes in its issuance of the Great Bay communities’ draft NPDES permits. EPA has elected to use its authority to override New Hampshire’s statutory water quality standard and insert its own judgment for that of the state legislature;”
  • “The public was largely shut out of the permitting process as EPA advanced its desired result in the face of criticism, opposition, counter-evidence, and repeated attempts to provide input;”
  • “EPA ignored repeated requests for public involvement and a more open process, and neglected to hold hearings or engage in a peer review process promulgated by EPA’s own policy;”
  • “Moreover, the Great Bay Municipal Coalition submitted numerous studies and pieces of evidence contradicting the science underlying the new standard, and the EPA ignored the information, without comment or response, and proceeded to draft the NPDES permits;”
  • “Internal communications and correspondence reveal that EPA was aware the science underlying the draft permit was suspect, but proceeded with the same stringent standards anyway;"
  • “The Great Bay Municipal Coalition has proposed a workable alternative to the proposed nitrogen limits that would limit the cost and reduce nitrogen in the estuary, but the EPA has not embraced this alternative.”

The findings in the memorandum are consistent with the concerns repeatedly brought forward by the Great Bay Municipal Coalition. These concerns revolve around a commonly shared interest of ensuring that the Great Bay estuary’s water quality is properly protected and that well-reasoned, scientifically justified and cost effective permit requirements are established for the area wastewater treatment plants.

The entire memo can be viewed here.

The hearing can be viewed below.


The Great Bay coalition communities have urged Congressional action by seeking an independent review of EPA actions, allege violations of scientific integrity policies.

The coalition has also requested that EPA Headquarters conduct an independent investigation of EPA Region I’s actions leading to the issuance of excessive nutrient reduction mandates for all communities in the Great Bay Estuary.

The Great Bay Municipal Coalition’s submission documented that Region I has violated federal research and science integrity policies. The Region also purposefully excluded the communities from the peer review process in an effort to push through the Region’s flawed regulatory agenda. These improper federal actions have great potential to cause harm to the public welfare and the environment by misdirecting scarce local resources to actions that will not meaningfully protect Great Bay. The Regional office nutrient reduction mandates are expected to cost the communities in the watershed nearly one billion dollars to achieve if they are not amended.

The letter from the Coaltion to the EPA can be viewed here: Letter of Scientific Misconduct to EPA;

A timeline of the nitrogen criteria development in Great Bay (attachment A of the letter) can be viewed here:Timeline, Nitrogen Criteria.

Exhibits to the letter can be viewed here (this is a large file consisting of hundreds of pages): Exhibits to Scientific Misconduct Letter;

Nitrogen and the Great Bay

The City of Dover recognizes that increased nitrogen levels in the Great Bay estuary are a concern. The City’s approach, along with coalition communities, is to reduce nitrogen levels.

The health of the Great Bay estuary has declined. An estuary is where fresh water and sea water mix. It is a dynamic, nutrient rich, diverse environment where many juvenile fish live before venturing into the ocean.

The indicators are:

  • Water quality in the Great Bay and tidal rivers has declined;
  • Nitrogen levels in the estuary have increased;
  • Eelgrass is disappearing;
  • Oyster populations are very low.

To protect and enhance this important resource, the City of Dover and coalition communities recognize it is necessary to lower the nitrogen load to the estuary to prevent algae blooms, and begin a watershed-wide nitrogen reduction effort.

Researchers estimate that 25 percent of the nitrogen reaching the estuary comes from the wastewater treatment plants. Seventy five percent of the nitrogen is believed to come from nonpoint sources such as septic systems, fertilizers applied for agricultural and landscaping purposes and stormwater runoff during rain events.

The City of Dover recognizes that action is needed, which is why it supports the AMP and additional scientific solutions to the problem, but at a cost significantly less than what would result from new EPA regulations.

Other science continues to support the City of Dover’s position.

Among the scientific data that aligns with the case made by the Great Bay Municipal Coalition is the recent State of the Estuaries Report by the Piscataqua Region Estuaries Partnership (PREP). PREP is part of the U.S. Environmental Protection Agency’s National Estuary Program, which is a joint local, state and federal program established under the Clean Water Act. PREP's goal is to protect and enhance nationally significant estuarine resources. PREP receives its funding from the EPA and is administered by the University of New Hampshire.

The report affirms the scientific analysis and continuing concerns of the Great Bay Municipal Coalition. In particular, the PREP report makes note of the fact that although dissolved inorganic nitrogen levels have shown a significant increasing trend at Adam’s Point since the mid 1970’s, there are no consistent patterns at other locations. The report shows that although the nitrogen load coming from wastewater treatment facilities within the estuary has remained relatively unchanged over the years there does appears to be a relationship between changing nitrogen load and rainfall.

Perhaps of most significance in the report is the acknowledgement of recent gains in eel grass growth. A declining trend in eelgrass was one of the main indicators upon which the NH Department of Environmental Services identified nitrogen as causing water quality impairment. Throughout the report, the need for additional research and data collection to understand cause and effect relationships impacting various indicators of water quality and the more recent trends and patterns of those indicators in Great Bay is noted.

The State of the Estuaries Report can be viewed here.

All of the most recent PREP reports, including a guide for citizens, can be found at the PREP website at

The Great Bay estuary

Often dubbed New Hampshire’s “hidden coast,” the Great Bay is unique because it is both a saltwater and freshwater system, or estuary, set apart from the coastline. The Piscataqua River brings salt water into the bay with the tides, an essential element for the growth of plant and animals that live in estuaries. Water levels in the bay are heavily influenced by these daily tides, which expose mudflats at low tide, providing important feeding grounds for birds. In recognition of Great Bay’s beauty, diversity and productivity, the U.S. Environmental Protection Agency has afforded special protection to it as one of only 28 “estuaries of national significance.”

Seven rivers that carry the pollution from 42 New Hampshire and 10 Maine communities drain into the Great Bay watershed, which comprises of 1,023 square miles. Sadly, the Great Bay estuary is showing signs of a failing ecosystem from this input. The 2009 State of the Estuaries Report, published by the Piscataqua Region Estuaries Partnership, showed 11 of 12 environmental indicators with negative or cautionary trends – up from seven indicators classified that way in 2006. (NHDES)

The state Department of Environmental Services maintains a page dedicated to the Great Bay estuary. That site includes numerous reports and studies pertaining to the health of Great Bay.

The page can be found here:

In 2009, NHDES issued a report titled, "Numeric Nutrient Criteria for the Great Bay Estuary," which looks at the nutrient levels in Great Bay. The report can be found here:

New Hampshire's nutrient standards

The EPA maintains information about each state's water quality standards, including numeric nutrient standards.

Each state, including New Hampshire, provides this information to the EPA.

New Hampshire, through the state Department of Environmental Services, filed a draft "Nutrient Criteria Development Plan" in 2002. This plan remains in draft form and is the basis for current nutrient measures.

The state's "Nutrient Criteria Development Plan" can be viewed here:

Other Documents: