'Toxic tides' of flesh-eating bacteria, cesspool runoff threaten Long Island's waters: Stony Brook report

Long Island waters are threatened by runoff from hundreds of thousands of cesspools, harmful algae and even flesh-eating bacteria, but opportunities for cleanup are "unprecedented," a prominent ecologist will tell residents, advocates and elected officials in an address Friday.

Stony Brook University Professor Christopher Gobler, whose laboratory monitors water quality across the region, will host the annual State of the Bays symposium at the Stony Brook Southampton Avram Theater on Friday at 7 p.m. He gave a preview at a news conference Tuesday in Riverhead.

What are the biggest problems and where are they?

Gobler’s lab identified dozens of water quality "impairments" in 2025 on Long Island’s coast and inland water bodies, ranging from a fish kill in Flushing Creek to toxic blue green algae blooms in Montauk. Roughly two dozen blue green algae impairments occurred on Suffolk’s East End. The lab also found occurrences of hypoxia (insufficient oxygen in marine waters), rust tide, paralytic shellfish poisoning and dinophysis, a type of algae that produces a biotoxin that accumulates in shellfish and can sicken people who eat them. On Long Island, dogs have become sick and died after drinking contaminated lake water and state environmental officials have closed some waters to shellfishing to protect the public. The western half of Shinnecock Bay is currently closed to shellfishing.

Compared with previous years, there were more locations of hypoxia and harmful algal blooms in 2025, but the size of a hypoxia zone in Long Island Sound was smaller due to long-term nitrogen load reductions, Gobler said in an email.

"We've been very fortunate on Long Island that more people have not been made ill by these toxic tides," said Adrienne Esposito, executive director of Citizens Campaign for the Environment, who heard a version of Gobler’s report several weeks ago that was aimed at environmental groups. "We need to be a lot more proactive to prevent future harm."

What about that flesh-eating bacteria?

It’s real, and it killed a Brookhaven man and two others in the New York City area in 2023. Though no deaths have been reported since then, Gobler said, the bacteria, Vibrio vulnificus, "is also present and a risk in our waters."

People can get infected by eating raw or undercooked shellfish, or by contact through an open wound. Typically, people who are infected will experience symptoms like vomiting and cramps, but for some, especially those who are immunocompromised, it can lead to lesions and limited blood flow to the tissue under the skin, which leads to cell death.

What’s behind the impairments?

One major underlying thread: roughly 360,000 aging septic systems in Suffolk County, and about 35,000 on Nassau’s North Shore, many of which leach nitrogen into water sources. The nitrogen feeds the algae, which gives rise to the blooms.

"All these individual septic systems are contributing thousands of pounds of nitrogen that are fueling these algal blooms and fueling these low oxygen conditions, and it's incredibly problematic," Gobler said.

Can anything be done about it?

Yes, according to Esposito and Gobler. An eighth-of-a-cent sales tax in Suffolk County, expected to generate $2.3 billion in coming decades for sewers and advanced septics, is starting to generate funds: $52 million already, according to Esposito. Between Suffolk and New York State programs, homeowners can get reimbursed for almost all costs of upgrading an old septic system. In Long Island Sound, nitrogen reduction practices shrank what Gobler said was one of the largest marine "dead zones" in the United States, so-called because of dangerously low oxygen levels, to 18 square miles.

Another piece of good news: aquaculture. On Long Island, it’s a relatively small industry of about 50 players, dominated by oyster farming, though there is growing interest in seaweed, said Michael Doall, associate director for bivalve restoration at Stony Brook’s School of Atmospheric and Marine Sciences.

Oysters and other bivalves feed on the algae and improve water quality; seaweed feeds on nitrogen and phosphorus. While the benefits don’t match the scale of those offered by sewer and septic improvements, they are significant and can be reaped much more quickly. Gobler said that one recent Stony Brook University study suggested that in Northport Bay, aquaculture can probably address 20% of nitrogen reduction needs.

"These are zero-input crops," Doall said. "They require no food, no fertilizers, no fresh water, no pesticides."