Rising temperature and chlorophyll, decreasing salinity, nitrogen levels above the Peconic Estuary Partnership standard, dense blooms of Alexandrium and Dinophysis, blue-green algal blooms in multiple ponds, and a few occurrences of fecal contamination characterized East Hampton Town water bodies in 2025, according to Christopher Gobler of Stony Brook University’s School of Marine and Atmospheric Sciences.
Dr. Gobler delivered an annual presentation to the town trustees, who for almost 15 years have engaged his lab to monitor water quality in water bodies under their jurisdiction, on March 9. Twenty-five sites were sampled, with analyses primarily done at the Gobler Lab at Stony Brook University’s Southampton campus, and data compared to state standards or federal recommendations.
While the surrounding open waters of Gardiner’s Bay, Block Island Sound, and the Atlantic Ocean mean the town’s waters are well flushed, “over the years, particularly the last decade or two decades, there has been a decent amount of development across East Hampton,” Dr. Gobler said, “and some of these water bodies are rather enclosed, so the land-use changes have the potential to impact enclosed water bodies.”
In a warming world, water temperatures are also rising, and temperatures in Accabonac Harbor, Hog Creek, Three Mile Harbor, and Northwest Creek exceeded the maximum for seagrass growth in 2025, Dr. Gobler said. “Summer tends to be a season where it’s warming faster than other seasons,” he said. Total nitrogen levels at sites in Accabonac and Three Mile Harbors as well as Hog Creek also exceeded the Peconic Estuary Partnership standard for seagrass in 2025.
“It varies by system,” Dr. Gobler said of nitrogen loading, with locations closer to the mouth of a harbor and the inlet of enclosed water bodies less likely to exceed the maximum for seagrass growth, but “high nitrogen shows you the effect of land-based nitrogen loading affecting these systems.”
He measured a “strong trend in chlorophyll,” which trends with the amount of nitrogen going from land to sea, telling the trustees that “things are definitely increasing from where we started, where the levels were relatively low.” This was particularly observed in Three Mile Harbor, Hog Creek, and Accabonac Harbor, he said.
Chlorophyll, he told the trustees, “is a proxy for the total amount of phytoplankton or algae in the water.” The National Oceanic and Atmospheric Administration and the federal Environmental Protection Agency “usually say you want don’t want to go above 20 micrograms per liter,” a level “at which you start having cascading ecosystem effects.” While most measurements were below that level in 2025, “there’s a few different sites in each of the different systems that do get above that,” including in Three Mile Harbor, Hog Creek, and Northwest Creek.
Activity on land affects groundwater, which then flushes into surface waters. Excessive nitrogen loading from land to sea, primarily from septic systems but also from fertilizer, “can be a strong driver for these ecosystems,” Dr. Gobler said. Excessive nitrogen loading leads to hypoxia, which can cause fish kills.
A bloom “of fairly large intensity” of Alexandrium, which produces saxitoxin, which can cause paralytic shellfish poisoning, was found in Three Mile Harbor in the spring and persisted at high levels for almost three weeks. “It’s not an all-time record, but it’s higher than we usually see,” Dr. Gobler said.
A “substantial” bloom of Dinophysis, which produces a gastrointestinal toxin less hazardous than saxitoxin but “nonetheless something we don’t want getting into shellfish,” was also seen in Three Mile Harbor in June and July. “That peak, I’m pretty sure, is the highest we’ve ever seen,” Dr. Gobler said.
Cochlodinium, or rust tide, “has been fairly ephemeral year to year” with wide variation, he said, but is trending in a good direction, with almost none detected in 2024 and levels “relatively low” in 2025.
In contrast to rising temperatures, surface water salinity levels are falling slightly, Dr. Gobler said. “That suggests a little bit more runoff from land to sea, depressing those levels,” he said.
Napeague Harbor “used to have almost undetectable levels” of fecal coliform bacteria,” Dr. Gobler said, but last year saw a measurement that greatly exceeded the State Department of Environmental Conservation’s maximum for shellfishing, with samples in Accabonac Harbor also exceeding the threshold. “Accabonac has really increased over time,” he said.
All freshwater bodies studied exceeded the E.P.A.’s algae standard, Dr. Gobler said, with chlorophyll in Wainscott Pond far above the E.P.A.’s 20 micrograms per liter maximum. Blue-green algae, or cyanobacteria, was also measured in high concentrations there as well as in Swan Pond and Pond Lane Pond, and in Fort Pond and Big Reed Pond in Montauk, the latter two outside trustee jurisdiction. Of Swan Pond and Pond Lane Pond, “These systems that bloom seem to be intensifying with time,” Dr. Gobler said. “Of course we worry about these, because they can make toxins that can be harmful to humans.”
Wainscott Pond has experienced worsening levels of cyanobacteria since Dr. Gobler began monitoring it in 2018. By 2023, “we went from having, like, a month of a bloom to, now, the whole entire year, April into December,” he said. The trend continued in 2025, he said.
Encouraging for the future ecological recovery of that pond, however, was the town’s 2024 purchase of 30 acres at 66 Wainscott Main Street. The site covers roughly one-third of the shoreline of the pond. With permission from the town and in collaboration with the Center for Clean Water Technology at Stony Brook University, “we started measuring the levels of nitrogen in the groundwater to this northern extent” of the pond, “trying to get a sense of how much nitrogen’s going in,” Dr. Gobler said, “and, can we do something about it?”
Last month, a proposal was submitted to the town to install a reactive barrier to intercept the high-nitrogen groundwater entering the pond along its northern shore. “There’s more to do than this,” he said, “but this, I think, is a great start.”
