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by Sabrina Artusa - February 8, 2026
Improved wastewater infrastructure and healthy shellfish populations are the keys to improving the water quality of Stony Brook Harbor. On Tuesday, Feb. 3, environmental activists and scientists gathered at the Stony Brook Yacht Club for a water quality forum, specifically focusing on Stony Brook Harbor.
Endowed Chair of Coastal Ecology and Conservation and Distinguished Professor at Stony Brook University’s School of Marine and Atmospheric Sciences Christopher J. Gobler spent the last two years monitoring water quality and shellfish populations in locations throughout the Stony Brook Harbor watershed. “We wanted to understand, what is controlling the growth of algae in Stony Brook Harbor?” he said.
Nitrogen is responsible for decreased water quality, causing hypoxic waters, or areas of low-dissolved oxygen, and harmful algae blooms that can be toxic. Gobler found that while nitrogen alone resulted in high levels of algae biomes, it was even higher when combined with phosphorus. “This is a nitrogen driven system,” he said.
“Most of the nitrogen in most of the watersheds comes from either on-site wastewater or fertilizer. For most of Suffolk County that is wastewater,” Gobler said. In a recently completed study, Gobler and his team aimed to isolate the cause of algae blooms. A proliferation of algae blooms, which thrive in nitrogen-rich waters, contribute to creating oxygen “dead zones” in water bodies where marine life cannot exist.
Nutrient-rich waters filled with nitrogen and phosphorus offer good conditions for phytoplankton growth, which leads to algae blooms. As the phytoplankton die, microbial degradation depletes oxygen from the water.
By studying water quality from several collection points in the harbor, Gobler found that sites “furthest away from the mouth of the harbor” are most prone to fresh water and high levels of algae.
For an area as heavily developed as Long Island, there are plenty of paved services that transport harmful substances into our waterways. Each speaker emphasized the importance of transitioning away from chemical solutions like fertilizer. Fertilizer accounts for 23% of the nitrogen load, second to on-site wastewater which tops the chart at 65.8%. Jimena Perez-Viscasillas, Outreach Coordinator for the Long Island Sound Partnership urged greener practices like cultivating lawns filled with native plants or using grass cuttings as a natural fertilizer.
Washing your car, too, can introduce grease and pollutants into the watershed. Using biodegradable soup and washing the vehicle on grass can help prevent unsafe chemicals from entering the water table through runoff.
Long Island is one of the few places that still disposes of waste primarily through septic tanks; 74% of Suffolk County residents use his method for disposing of waste.
The on-site treatment devices separate solids from liquid. The septic tank will store solids in a compartment while allowing the liquid to enter a leaching pool of soil that acts as a filter. Gradually, the liquid will cycle down into our groundwater, which then seeps into the aquifer – the source of our drinking water. It does not treat nitrogen in a targeted way, as innovative and alternative on-site wastewater Treatment systems do.
The Long Island Garden Rewards program will reimburse people for up to $500 if they install rain gardens, native plants of rain barrels. Further, residents can be reimbursed for replacing their septic system with an innovative and alternative on-site wastewater treatment systems. Go to https://suffolkcountyny.gov/Departments/Public-Works/Septic-Improvement-Program for more information.
Looking forward
There is still work to be done when it comes to water quality. The speakers noted that the recent progress is cause for commendation. Long Island Sound Partnership surpassed their goal set in 2001 of diminishing nitrogen inputs from wastewater treatment plants by 58.5%. Sustainable and Resilient Communities professional Elizabth Hornstein said they have achieved a 69.1% reduction. “We are more focused on now addressing on-site septic systems like Chris was just talking about, also trying to capture and treat stormwater runoff through green infrastructure projects, as well as even supporting projects to remove nitrogen that is in our waterways by growing shellfish and seaweed through what is called bio extraction,” she said.
Nutrient-rich waters can also impact the coastal environment and contribute to marsh deterioration. Stony Brook Harbor, designated a significant coastal fish and wildlife habitat by the state, is home to many organisms. Some of these populations, like clams and other bivalves, are decreasing. Gobler said mussels are on track for extinction in New York. Lobsters, which formerly resided in Long Island waters, have since migrated north to colder waters. Climate change, Gobler said, is the cause. The effect is most prominent during the summer, when peak temperatures are increasing.
However, there are still ways to improve our water quality. Oyster populations have increased since 1970, said.
Carl Safina, founder of the environmental nonprofit The Safina Center and Endowed Research Chair for Nature and Humanity at Stony Brook University’s School of Marine and Atmospheric Sciences, emphasized that there are still ways to improve water quality. “Why is [Chris] still talking about shellfish and oyster restoration?” he asked. “Because it is still possible.”
Adrienne Esposito, the executive director for Citizens Campaign for the Environment and policy chair for the Long Island Sound Partnership Citizens Advisory Committee, said following the comprehensive plans and rejecting development can help the County achieve its goal of reducing nitrogen in Stony Brook Harbor of 37%. “You know what the plan doesn’t say,” Esposito said of Suffolk County’s Subwatershed Management Plan . “It doesn’t say keep building and build sewage treatment plants and discharge them into the Stony Brook Harbor. It doesn’t say that anywhere, and yet those are the proposals we see.”
In 2022, Smithtown approved a subdivision proposal that would allow Gyrodyne, LLC. to develop a 250-unit assisted living facility, a 125-room hotel, a 153,110 square foot office building, a sewage treatment plant and a parking lot. In August, they sold 9-acres of the property to B2K Development.
“There is no reason for these plans to go forward when the funding to buy this land exists,” Suffolk County Legislator Steve Englebright (D-Setauket).
“We are in this conundrum on Long Island, as Dr Safina pointed out on Long Island where we have a limited ability…We have overbuilt on Long Island. We are degrading our drinking water. We are degrading our beaches and our harbors and our bays and our estuaries. We are adding more and more wastewater and we can’t continue like this,” Esposito said. “We have to make choices.”
Nonetheless, she said Suffolk County is making progress–hiring more environmentalists and pushing residents to transition from septic systems.
“The challenge for us is to figure out how we can sustain Long Island without losing what we love about where we live, which is the fact that we get to live by the water,” Esposito said.
