Nitrogen pollution is killing eelgrass and threatening aquatic life in Great Bay, and environmental groups are taking action.

In 1972, under increasing pressure to protect the nation’s vital waters, the federal government passed the Clean Water Act. Section 303(d) of that statute requires states to develop lists of “impaired waters.” These are waters in which existing regulations are not stringent enough to maintain water quality standards.

The N.H. Department of Environmental Services has identified the Great Bay Estuary as impaired, and the U.S. Environmental Protection Agency is expected to approve that designation within the next couple of weeks.

“We’re still in the about-to-do-that category, but it’s kind of a given that that’s going to be the result,” says Paul Currier of the DES. “We’re under the gun, so it’s going to be shortly.”

The Great Bay Estuary and its precious beds of eelgrass provide important breeding and nursing grounds for a colorful array of species, including lobsters, striped bass, oysters, horseshoe crabs and waterfowl. But a rising load of nitrogen flowing into the estuary from wastewater treatment facilities, septic systems and storm water runoff is decimating eelgrass habitats and threatening local wildlife. 

The EPA listing will affect permitting for wastewater treatment plants and development projects. It will also force local communities to reevaluate how they deal with storm water runoff and sewage. The local impact is likely to be significant, but the cost of inaction could be even greater. “The scientific consensus is that Great Bay is right at the tipping point,” Currier says. “If we don’t do something, Great Bay may well lose a lot more of its environmental integrity.”

the problem

Great Bay is New Hampshire’s largest estuary, a tidal confluence of freshwater rivers and saltwater ocean encompassing close to 11,000 acres, including the Piscataqua River, Great Bay and Little Bay. It has seven tributaries: the Bellamy, Cochecho, Lamprey, Oyster, Salmon Falls, Squamscott and Winnicut rivers. The 144-mile shoreline consists of wooded banks, rock outcroppings, shale beaches and salt marshes bordering numerous communities. The estuary’s watershed covers roughly 930 square miles, stretching inland up the Salmon Falls River to Milton and along the Lamprey River to Candia.

Within this estuary resides a complex network of symbiotically connected organisms. It serves as a nursery for lobsters, crabs, winter flounder, cod, pollock, eels and hake. Juvenile and adult striped bass can be found feeding on smaller baitfish like silversides and smelt. The estuary is also crucial habitat for oysters and other shellfish. These aquatic organisms, in turn, feed waterfowl and other birds, including some endangered or threatened species such as bald eagles, common terns, upland sand pipers, marsh hawks, ospreys and common loons. Several mammals also rely on the estuary, including otters, beavers, minks, muskrats and harbor seals. It’s a sign of nature’s delicate balance that changes to one species have an almost unpredictable ripple effect on all the others. If the estuary’s eelgrass goes away, it will eliminate “really critical habitat for juvenile fish species and waterfowl,” says Dave Kellam, project coordinator for the Piscataqua Region Estuaries Partnership. That means a variety of other creatures farther up the food chain suffer, too.

And here’s the scary thing: the eelgrass is going away. Rapidly. According to Phil Trowbridge, coastal scientist for the Estuaries Partnership, eelgrass in Great Bay declined by 37 percent between 1990 and 2008. Portsmouth Harbor has experienced a 25 percent decline. Eelgrass has “disappeared entirely” in tidal tributaries such as the Lamprey, Oyster and Squamscott, and the aquatic plant has all but vanished from the Piscataqua River and Little Bay. Unlike seaweed, eelgrass is actually rooted in the soil. Like plants you might find in your backyard, it converts sunlight into biomass and produces oxygen. In fact, eelgrass is one of the “dominant primary producers” of oxygen in Great Bay, Trowbridge says. The repercussions of losing eelgrass are far-reaching. “In the short term, you lose habitat, and that affects the animals that use that habitat,” Trowbridge says. “In the long term, the loss of eelgrass presages a more significant change in the food web.” 

So, what’s causing the eelgrass to die off? The process is called eutrophication. It’s caused by abnormally high concentrations of nitrogen in the water, leading to a proliferation of nutrients that give rise to algal blooms. “Algae in the water feeds on those nutrients and their populations increase dramatically,” Kellam says. “Now you have all this algae in the water and it does a couple of things. One, it makes the water cloudy, and that cloudy water prevents sunlight from penetrating as deep as it should.” Without sunlight, eelgrass can’t survive. Secondly, when the eelgrass and algae dies, it decomposes. That process actually pulls oxygen out of the water as it’s absorbed by microbes, leaving insufficient oxygen levels for other organisms. “Basically, it suffocates fish and other things living in the water,” Kellam says.

It’s difficult to assess the toll eutrophication has already taken on the estuary. Fish populations are affected by a variety of factors that are not easy to quantify. Oyster beds in Great Bay have been shrinking dramatically for several years. It’s unknown, though, whether that’s a result of declining eelgrass or one of its causes. Oysters filter water and make it clearer, so losing them could have an adverse effect on eelgrass populations. “Everything is somewhat synergistic,” Trowbridge says. “It’s really hard to see a one-to-one correlation.” So far, scientists monitoring Great Bay have not noticed a dramatic reduction of dissolved oxygen. But oxygen is declining in the seven tributaries. Nitrogen levels in Great Bay have skyrocketed by 44 percent over the last 28 years, and the nitrogen load entering the estuary has increased by 42 percent over the last five years.

“They haven’t seen the effects of eutrophication, but you see the equation,” Kellam says. “This can’t go on forever.” The same type of pattern has caused major problems in the nation’s largest estuary, Chesapeake Bay, bordering Maryland and Virginia.

Eutrophication in Chesapeake Bay has decimated blue crab populations since the 1970s. In fact, nitrogen pollution is a moderate to severe problem in almost every estuary in the United States, spurring the U.S. Environmental Protection Agency to make it a top priority since the 1990s. “It’s the number one nationwide problem in terms of estuaries,” Trowbridge says.

the solution

Solving the problem, at least theoretically, entails limiting the discharge of nitrogen into the estuary and its surrounding rivers. Doing that will require a range of regulatory measures and educational outreach initiatives. According to Kellam, research shows that 31 percent of the nitrogen entering Great Bay comes from wastewater treatment plants in the area, while 65 percent comes from “non-point sources” like storm water runoff, septic systems and fertilizers. Keep in mind, nitrogen is a natural element vital to all life on earth. Inert nitrogen gas makes up about 80 percent of the atmosphere. A portion of this nitrogen is converted into forms that enter soil and water and feed plants, which are then consumed by animals. Eventually, that nitrogen returns to the soil through animal waste or when organisms die and decay. Nitrogen in soil and water ultimately converts back to a gas and returns to the atmosphere, where the cycle begins anew. Even excess nitrogen dumped into the atmosphere by power plants, vehicle exhaust and other polluting sources can be processed by nature if it falls on undeveloped land. But impermeable manmade surfaces like pavement or rooftops prevent nitrogen from filtering through the soil and returning to the atmosphere. Instead, storm water runoff washes it directly into the estuary or nearby rivers.

“The deal with nitrogen is that the only way to get it out of the water is to have a biological process. Either plants eat it up or bacteria eats it up,” Kellam says. But if it’s not made available to soil, “then the nitrogen is going right into the estuary, and that’s the crux of the problem.” Inclusion on the EPA’s list of impaired waters could have an array of effects on the facilities and developments surrounding Great Bay. “The first and most immediate one is going to be an effect on the permit limits for wastewater treatment plants,” says Paul Currier, of the DES. Wastewater treatment facilities around the greater Seacoast will face stricter limits on the amount of nitrogen they’re allowed to discharge into the estuary. The first plants to be affected will be those in Portsmouth and Exeter.

Portsmouth’s treatment plant on Peirce Island discharges an average of 4.5 million gallons of wastewater per day into the Piscataqua River. In 2007, with urging from the Conservation Law Foundation, the EPA ended a practice allowing the plant to operate with only primary treatment of wastewater. The plant is in the process of acquiring a permit renewal, which will include standards for secondary treatment. Because of the “impaired” designation, that treatment will include reducing nitrogen output. The Department of Environmental Services is working on determining a total maximum daily load for area facilities, putting limits on the amount of nitrogen they will be permitted to discharge. Those numbers will also affect the plant in Exeter, which is up for permit renewal this year. Both plants are waiting on the DES to establish nitrogen limits before finalizing their permits. “We are working on that as fast as we can, recognizing that there are time constraints,” Currier says.

Several technologies exist to reduce nitrogen levels in wastewater. One tactic involves introducing bacteria to the pipelines to consume nitrogen content. “There are some upgrade technologies that they can install,” Kellam says. The new technology will factor into Portsmouth’s design for a new wastewater treatment facility. The city plans to replace the plant on Peirce Island with a new facility at an undetermined location.

Representatives from the Department of Public Works could not be reached last week and did not return phone messages. Kellam says installing nitrogen removal technology will be an “expensive prospect.” But the costs are not crippling, according to Melissa Hoffer, vice president and director of the Conservation Law Foundation’s N.H. Advocacy Center. “There are ways of addressing and reducing nitrogen that are cost feasible,” she says.

Down the line, all sewage plants across the region will have to conform to the new regulations. Wastewater treatment facilities in New Hampshire typically operate on five-year permits. The U.S. Department of Agriculture recently awarded $10.5 million in funding to upgrade the treatment plant in Farmington. “They will all come up for renewal, and as they come up for renewal, that will be the opportunity to ensure that appropriate nitrogen limits are built into them,” Hoffer says. If sewage plants can figure out ways to reduce nitrogen output to a sustainable level, the estuary can absorb the rest. “There’s this benefit of being able to basically process our wastewater if we can get it all balanced out,” Kellam says.

But reducing nitrogen in wastewater is only part of the solution. The Great Bay Estuary’s plight will also call for strict permitting regulations on new development and processes for dealing with storm water runoff. the community impact

The estuary’s “impaired” listing could have the effect of deterring developers from pursuing projects in the Great Bay region. Implementing technologies to deal with storm water and meet the new criteria for building permits will be expensive. “That’s why it’s a big deal, because it is going to add a layer of cost to things,” Kellam says.

The regulatory impacts this new designation will have on residential homes and businesses, if any, remain to be seen. Any bans on fertilizers or other environmental mandates would have to be approved by the state Legislature. But saving the estuary will also call for voluntary efforts from individual citizens. Homeowners must maintain their septic systems and regularly have them inspected and pumped. They should also minimize use of lawn fertilizers and other chemicals. Landscaping with native plants that are adapted to the local climate can help. Residents should also minimize impervious surfaces around their homes and make sure storm water runoff discharges into areas where it can infiltrate the ground. Porous surfaces can be used for driveways, and rain barrels can collect runoff from rooftops for use in home gardens.

“The longer we give a chance for the water to percolate through soils, the more chances we have of eliminating the nitrogen,” Phil Trowbridge says. Recent state legislation could also help the estuary. On July 15, Gov. John Lynch signed Senate Bill 168, establishing the Southeast Watershed Alliance. The alliance is intended to address threats to the Great Bay Estuary, including nitrogen pollution from wastewater treatment plants, storm water runoff and sprawl development. The Conservation Law Foundation strongly supported the legislation, saying it would help generate region-wide solutions to the problem. “It will provide a much-needed vehicle for cities and towns throughout the watershed to work together, with guidance from state and regional agencies, to address the challenges facing this unique and sensitive resource,” staff attorney Kristine Kraushaar said in a press release.

Lynch also signed a number of other bills geared toward protecting rivers, including House Bill 58, which adds the Cochecho River to the state Rivers Management and Protection Program. Although eelgrass beds have already incurred significant damage in the Great Bay Estuary, Phil Currier believes we can save the habitat if we take appropriate actions now. “I think there’s plenty of opportunity for the bay to recover. The Great Bay is in better shape than lots of the other estuary systems that are already substantially eutrophied,” Currier says. But, he adds, “This is not gonna be quick.”

What’s more, even if we decrease the amount of nitrogen flowing into the estuary, it does not guarantee that eelgrass populations will recover. “There are lots of factors that affect how eelgrass grows, and one of them is nitrogen,” Currier says. “There are other factors, as well, so whether or not you see a direct restoration if we reduce the nitrogen—I don’t know.”