In what’s become an annual warning to Long Islanders about the health of Long Island’s waters, Stony Brook Chair of Coastal Ecology and Conservation Dr. Christopher Gobler is again asking for the public’s help in addressing one of the greatest threats to coastal ecosystems — on-site septic systems.
Dr. Christopher Gobler at the April 21 press conference on the Peconic riverfront. |. Denise Civiletti photo/Riverhead Local
Dr. Gobler outlined the latest issues at a press conference on the downtown Riverhead waterfront Tuesday, in advance of his State of the Bays address Friday at Stony Brook Southampton.
“There are incredibly pressing problems when it comes to water quality here on Long Island, but at the same time, we have some incredible opportunities to address those problems, in a way that’s unprecedented in the history of Long Island,” he said.
Dr. Gobler pointed out that more than two dozen lakes and ponds on Long Island suffered from toxic blue-green algae blooms in 2025, and five different locations in local marine ecosystems were closed to shellfishing last year because of blooms of the plankton Alexandrium, which produces saxitoxin — a poisonous chemical that causes paralytic shellfish poisoning.
“We had one situation in Southold where the levels of saxitoxin in the shellfish were so high that they would have resulted in an extreme sickness and potentially even death if someone had consumed those shellfish,” he said. “Thankfully, the New York State Department of Environmental Conservation was on the case and proactively closed that place to shellfishing. No one got sick because of their great work. But the fact of the matter is that’s a very dangerous situation.”
Dr. Gobler said that three dozen other locations throughout Long Island’s waterways are routinely suffering from oxygen levels so low they’re called “dead zones.”
“Every hour that a water body spends below three milligrams per liter (of oxygen) is an hour that is doing harm to marine life, and in my seminar on Friday, I’m going to show how there’s a direct linear relationship between low oxygen and poor outcomes for marine life, and specifically our shellfisheries,” he said.
Dr. Gobler said 2026 is not off to a great start, with three creeks in Southold now closed to shellfishing again, along with the entire western half of Shinnecock Bay, due to high levels of Alexandrium.
Algae blooms tend to be more common as water temperature rises, but that’s not the case with these blooms.
“Despite that cold winter, the algal blooms are not waiting for the conditions to warm up,” he said.
He also said local researchers are on the lookout for the bacteria Vibrio vulnificus, also known as “flesh eating bacteria,” which he said has “slowly moved up the East Coast” after having existed only in the Gulf of Mexico for a very long time.
“There are certain hot spots on Long Island, and it’s a complicated story. There are multiple environmental drivers,” he said.
Dr. Gobler suggested people wear foot protection when swimming in water, and advised that elderly people, and those who are immunocompromised, stay out of the water.
“I’m not going to sugarcoat it,” he said. “People who are infected with this bacteria have a 20 percent chance of dying within just 48 hours following infection. It’s very, very serious.”
Signs of Hope?
Dr. Gobler’s fellow Stony Brook researcher Michael Doall said he’s seen promise in his work with local aquaculture — mainly of oysters — and seaweeds, which can remove the nitrogen from surface waters, decreasing the severity of algae blooms.
“They’re really the only zero input crops out there,” said Mr. Doall at the press conference. “When you’re talking about vegetable crops on land, or livestock, you either fertilize it or you have to feed it. Even fish farming, you have to feed fish. But seaweed and shellfish are absolutely zero input crops. Instead of feeding them, they get their nutrition from the waters around them, and in so doing, they’re taking nitrogen out of the water. We refer to this as nutrient bioextraction, and it’s a big part of the solution for Long Island.”
Mr. Doall said plans to upgrade Suffolk County’s septic systems to remove nitrogen “are going to take decades.”
He added that the nitrogen from septic tanks is already in Long Island’s groundwater, and can take still more decades to reach surface waters.
“We need a solution right now to mop up the mess in the water,” he said, adding that about 50 different farms across Long Island are already doing this work.
The County Has Money
Suffolk County Deputy County Executive Jennifer Juengst also outlined the county’s funding for upgrading septic systems. The county has been working to remove 360,000 cesspools and non-functioning septic systems, though a septic upgrade pilot program, but has only replaced several thousand systems to date.
She said that, due to new funding sources including a recently instated 1/8 penny sales tax for the county’s Water Quality Restoration Fund, which is expected to raise $2 billion for water quality over the next 35-40 years, Suffolk is now “the only county that we know of in the United States that is nearly funding 100 percent of the cost of these systems.”
She added that the county will next month roll out an online application to make it easy for people to apply for its Septic Improvement Program.
“Conceivably, you could get almost 100 percent of your system paid for,” she said.
Dr. Gobler, who heads Stony Brook’s Center for Clean Water Technology added that the center’s data on its nitrogen biofilter septic system upgrade has “performed just as well as any of the commercial IA [septic] systems.”
He said plans to produce biofilter systems at low cost are “not quite as low as we hoped. The cost for our systems to be installed are generally in the range of the other systems.”
“We’re continuing to innovate, and in the pipeline, we have more systems that are coming up that we think will be even more cost effective,” he said. “We’re hoping we will shatter the glass ceiling of cost.”
Denise Civiletti from Riverhead Local contributed reporting for this story.
Register to attend the State of the Bays address Friday at Stony Brook Southampton.
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Growing up in New Suffolk, I have watched the amount of horseshoe crabs dwindle to almost nothing during mating time in the spring all for use as bait for conch and eels because they’re available. They have around for 450 million years. Should we make them disappear so someone has easy bait?
I think not.