Dozens of privately owned sewage-treatment plants have violated pollution standards repeatedly over a four-year period by discharging excessive amounts of nitrogen into Suffolk County’s ground and surface water, a News 12 Long Island/Newsday investigation found.

The county health department, meanwhile, has only imposed a few thousand dollars in fines on even the top polluters, which have dumped excess nitrogen almost every month from 2011 through 2014, according to a Newsday analysis of Suffolk records.

Sixty plants — including apartment complexes, condominium associations, nursing homes and commercial buildings — had 10 or more months between 2011 and 2014 in which they violated nitrogen standards, the records show. And 22 of those plants reported higher-than-allowed amounts of nitrogen in at least half of their monthly tests during that period. Nitrogen-discharge levels during some months were as much as 10 times higher than allowed, a sign that the waste-treatment plants weren’t working properly, experts said.

High levels of nitrogen in bays, rivers and other waterways have been linked to harmful algal blooms that can kill marine life and close beaches. Nitrogen in groundwater is regulated by the federal Environmental Protection Agency and the state because of possible health effects among pregnant women and infants.

County Executive Steve Bellone has declared nitrogen to be “public water enemy” number one and is his top environmental concern as he seeks to expand sewer lines and approve advanced septic systems for single-family homes.

“Nitrogen poisoning of our surface and groundwaters is the greatest crisis this county has faced in generations,” he said in his 2014 State of the County speech.

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But the sustained violations and a recent change that allows new sewage-treatment plants (STPs) to be located closer to public water wells has some concerned that the county is not doing enough to protect the groundwater from nitrogen.

Christopher Gobler, a professor at Stony Brook University’s School of Marine and Atmospheric Sciences, said, “The county has begun to take ownership of the nitrogen issue, but there needs to be oversight of all aspects. The STPs need oversight and regulation.”

The Suffolk County Water Authority tests and treats water to ensure what comes out of taps is below the nitrogen limit of 10 mg per liter, sometimes by diluting the water or, on rare occasions, treating it to remove nitrogen.

Nitrogen levels in Long Island’s aquifers have been rising. For example, concentrations in the Magothy aquifer, one of the two shallower aquifers that provide most of Long Island’s drinking water, increased more than 80 percent between 1987 and 2013, according to the county’s Comprehensive Water Resource Management Plan released this year. The prime drivers are septic systems on homes, followed by fertilizers placed on farms and lawns, according to the report.

More than 150 privately owned treatment plants have sprung up in Suffolk over decades, approved to treat the waste created at dense developments like apartments and condominiums, office buildings, malls and nursing homes. Operated by outside companies and overseen by engineers, they operate under state permits. The county regulates and monitors the plants, including their nitrogen discharges.

Top violator North Isle Village, an apartment complex in Coram, exceeded nitrogen standards every month between 2011 and 2014. It was fined $6,000. Another top offender, the Suffolk Center for Rehab and Nursing in Patchogue, exceeded nitrogen standards 46 out of 48 months. It was also fined $6,000. MacArthur Plaza, a commercial office building at 2540 Veterans Hwy. in Holbrook, violated nitrogen standards for 33 months in the four-year period. It was fined $2,000.

Data for 2015 was not available for all the plants the county monitors.

The county has the power to fine polluting plants up to $2,000 a day. But Suffolk has typically exempted plants from the fines that agreed to “orders on consent” — improvement plans filed in court. Those plans can sometimes span years.

Walter Dawydiak, director of the county’s division of environmental quality, said big fines could be a burden on some plant owners, particularly those owned by residents, and delay improvements.

“We try again not to be punitive or to raise revenue. The goal is to have a working relationship that fosters compliance with the regulating community.”

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Adrienne Esposito, executive director of Citizens Campaign for the Environment, said the county needs to aggressively crack down on for-profit owners like nursing homes and commercial centers that are polluting.

“The county has taken too much of a lackadaisical approach to fining profit-making entities for polluting groundwater,” she said. “This is part of the problem on Long Island. It has become acceptable to pollute and we desperately need to change that.”

She said a state environmental fund should make low-interest loans available to nonprofit owners, like condominium associations in low- or middle-income areas.

The county Department of Health defended its regulation of sewage treatment plants and has called its overall compliance program a success.

The number of plants found by the county to be out of compliance and under legal action to upgrade has dropped, from 35 in 2012 to 23 in 2014 and 19 today, Dawydiak said.

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All the privately owned plants that treat for nitrogen are on track to be brought into compliance with their state permits by 2017, Dawydiak said.

Overall, the nitrogen levels of water discharged also have been reduced since 2012, when budget cuts reduced the county health department’s inspection staff by an engineer, inspector and clerical position. The county decided to focus inspections on “high risk” plants as it dropped inspections of “low risk” facilities that had a history of compliance.

In 2011, 71 percent of STPs designed to reduce nitrogen met state discharge limits. In 2014, 84 percent met those limits, according to an annual report released in November.

Old systems that had been “nursed along are now at the end of their useful life and we’re working with the communities to upgrade those,” Dawydiak said.

After months of defending its record on sewage treatment plants, the county announced late last month that it would review its enforcement practices “to identify opportunities to further strengthen its regulatory programs.”

It has been holding meetings with environmentalists, the Suffolk County Water Authority and state Department of Environmental Conservation, the county said in a news release.

Joseph Pokorny, deputy CEO for operations for the Suffolk County Water Authority, the largest water provider in the county, said sewage treatment plants should not be dumping excess nitrogen in the water.

“There should be enough of a fine to make them change their behavior,” he said. But most importantly, he said, “I’d like to see more compliance.”

Still, he said sewage treatment plants are generally preferable to septic systems, which involve no treatments.

Bob DeLuca, president of environmental advocacy organization Group for the East End, said county oversight will be increasingly important as it expands sewer lines and approves new nitrogen removal systems for single-family homes. That means county staff who can work with operators on sometimes complex systems.

“Whenever you don’t have enough people to look after the facilities, problems like this are likely to happen,” said DeLuca, who worked for the county division of environmental quality in the 1980s and 1990s. “As the county moves toward substantive treatment, we have to have the guys who can go in and make sure things are working properly.”

Critics also questioned the county’s decision to make it easier for new sewage treatment plants to be located closer to public water wells — where discharge could reach public water sources in two years. An earlier draft of the county policy had proposed a restriction where new plants must be constructed in areas where it would take treated water at least 50 years to reach a drinking water well.

That 50-year proposed policy, written in 2010 for the county’s water plan, was meant to separate treatment plants from drinking water sources. But on May 5, 2014, the county Division of Environmental Quality staff proposed a 2-year policy in a memo, which later was adopted as part of the comprehensive water plan.

Dawydiak argues that the 2-year standard is sufficient and exceeds state health standards. Pathogens, such as bacteria, will die in that time, he said.

“It’s a complicated issue. All of us would like to see no nitrogen at all go into any area where it could have an impact. But as a practical matter, there are people here, and we excrete nitrogen,” he said. In the past 15 years, none of the 68 STP sites have been located closer than the 25- to 50-year travel time to public supply wells.

Pokorny said that the SCWA was not consulted before the policy was written, but has been assured in recent meetings that they would be consulted on the location of new sites.

Most of the owners and operators of the top polluting sewage treatment plants did not return calls or declined to comment.

One who did was Robert Heppenheimer, owner and executive director of the Nesconset Center for Nursing. He said he depended on an outside contractor to maintain and operate the nursing home’s plant and was unaware of the extent of the problems.

“I’m reliant on operators and engineers to keep me in compliance,” he said. “It’s been my goal to always be in compliance.”

Heppenheimer said he spent $1.5 million to upgrade the sewage treatment plant when he bought the nursing home in 2008. He thought the plant would be in compliance for as many as 20 years. Instead, from 2011 through 2014, it violated nitrogen standards 33 of the 48 months and three out of the first six months of 2015.

He dismissed his operator, Pure Process of Selden, in November 2014.

Pure Process owner Richard Flohr Jr., whose name is listed on the state permit, said the plant’s failure was not his fault. He said operators can recommend improvements, but owners are sometimes loathe to pay. “They like to put the blame on us,” said Flohr. “We can recommend something, and it takes two or three months for them to pay.”

Getting plants to work properly involves a lot of factors, he said. “There are so many variables out there. The pH, the temperatures,” he said. “It’s just not something you go to the bathroom, flush and it’s done and going to be perfect every day.”