Long Island beaches and bays: What's improving, what's not

For 17 years Crescent Beach in Glen Cove was closed to swimmers because water testing showed bacteria levels exceeded the state health standards. The source of the bacteria was finally traced to a couple of pipes leading from two nearby ponds with large populations of waterfowl, according to Nassau County Legis. Delia DeRiggi-Whitton.

During heavy rains, their droppings were swept up in stormwaters and carried from those pipes to a stream that flowed into the Sound. Droppings from dogs, raccoons and other animals probably contributed as well, she added.

After a series of stormwater management improvements — including filters installed on the pipes, a new drainage pipe to help circulate water and plantings that absorb bacteria — bacteria levels dropped and last month the beach was reopened for the first time in nearly two decades.

"I think it’s really a success story about different levels of government working with environmental groups and neighbors to make this happen," DeRiggi-Whitton (D-Glen Cove) said. "It’s a very peaceful, beautiful beach."

While tens of thousands of Long Islanders enjoy the water every year, there are also red tides of algal blooms, and the rare report of life-threatening bacteria in the water.

Long Island’s bays and beaches have been troubled for decades by water quality problems — algal blooms and low-oxygen zones as well as bacterial contamination. In some places, infrastructure projects, from filters like the ones in Glen Cove to large sewer systems, have brought significant improvements. But there are still water quality concerns, some periodic, some chronic, that experts say need attention.

Here's a rundown of the good and not-so-good news.

Which water quality problems are improving?

Algae, a group of plantlike organisms, grow naturally in fresh and salt water — from long, spongy kelps to microscopic phytoplankton — and there is nothing inherently harmful about them. On the contrary, they absorb carbon, produce oxygen and form a vital part of fresh water and marine food chains. 

But under certain conditions — warm temperatures, heavy nutrient loads and stagnant water — they can proliferate so much that they cause harm to ecosystems and to human health.

Some types of algal blooms have diminished in recent years. 

Chris Gobler, a professor at Stony Brook University’s marine sciences department, said in his annual "State of the Bays" lecture in April that there have been fewer brown and rust tides in recent years. These are considered "ecosystem disruptive": they block sunlight from penetrating the water column, and as they die and decompose they consume oxygen. In severe cases they can kill sea grass and marine animals. But they don’t generate toxins that are dangerous to humans and other terrestrial animals. 

A related improvement: The Sound’s areas of low oxygen are shrinking. Called hypoxic zones, these most often appear where excess nutrients like nitrogen and phosphorus encourage heavy algal growth; when the algae die and decompose, dissolved oxygen levels in the water plummet — causing die-offs and slow growth for bivalves, fin fish and crustaceans. Between 1987 and 1999 hypoxic zones in the Sound spread across 208 square miles on average, according to Long Island Sound Partnership, a collaboration of federal, state and local government agencies and environment groups.

Between 2021 and 2025, the average was 83 square miles, and last year the size of the zones decreased to an all-time low, at 18 square miles. The partnership’s models suggest that this year the zones may shrink again, to about 15 square miles. Officials and ecologists attribute the decline to the construction of sewers in western Nassau.

More frequent sightings of large marine animals around Long Island are sometimes attributed to cleaner waters. But the main driver of those population increases, according to Carl Lobue, a senior marine scientist at The Nature Conservancy, was the resurgence of menhaden or bunker, a favorite prey for spinner and hammerhead sharks, humpback whales and dolphins. Their populations rebounded after limits were placed on their harvest five years ago. 

LoBue said menhaden numbers are falling again, leaving some marine predators and fish-eating birds like ospreys malnourished.

What’s not so good?

Like Crescent Cove, some Long Island beaches and bays are periodically closed because of high bacteria levels — which can almost always be traced to human or animal feces. The source can be stormwater runoff, faulty septic systems or leaking sewer lines, according to Peter Linderoth, director of healthy waters and lands at Save the Sound.

Runoff problems can be addressed with infrastructure that allows more rainwater to get absorbed in the ground. Green infrastructure projects that hold and absorb rainwater, such as bioswales (shallow channels planted with hardy native plants), rain gardens, green roofs and permeable pavement — "those all go a long way to reducing the stormwater impacts on our coastal waters," Linderoth said.

Also, while brown and rust tides have diminished, several types of algae that can produce toxins harmful to humans and other animals remain a concern.

These microorganisms drift widely and mostly harmlessly in coastal waters until they find the warm and nutrient-rich conditions that foster rapid growth of both the algae and the toxins they sometimes harbor, forming what are often called toxic algal blooms.

High concentrations of Alexandrium, a type of algae that can make a powerful neurotoxin called saxitoxin, have led to shellfish closures in Shinnecock Bay and elsewhere in recent years. Last year cell densities of Alexandrium in Jockey Creek, which empties into Southold Bay, far exceeded the state record for several weeks, Gobler said. Tissues of shellfish taken from the creek also had very high levels of saxitoxin — 22 times higher than the U.S. Food and Drug Administration's closure limit, according to data from the state Department of Environmental Conservation.

What about reports of 'flesh-eating' bacteria in Long Island waters?

It’s true that a microbe called Vibrio vulnificus, which thrives in warm, brackish water, has now been detected as far north as Maine, as ocean temperatures have risen. And it’s true that it can cause serious infections — and rapidly decaying tissue — especially in immunocompromised people. But Gobler said in his annual "State of the Bays" lecture in April that so far these bacteria have generally been found in very low densities in New York — the bacteria require just the right conditions of warm water and lower salinity to reach dangerous concentrations, he said. 

One Suffolk County resident and two in Connecticut died of Vibrio vulnificus infections in 2023. Gobler said the chances of contracting a fatal infection are very slim.

"You are 50 times more likely to drown than you are to get one of these infections," he said.

He noted that his children, now grown, learned to swim off Long Island's beaches and that he continues to plunge in without fear. 

What’s the long-term forecast for Long Island’s water quality?

On the one hand, experts expect Suffolk County’s investment in advanced septic systems and sewers to gradually reduce nitrogen loading in local coastal waters. And green infrastructure projects like the ones in Glen Cove can successfully address bacterial contamination from stormwater runoff. But global trends are working at cross purposes to local ones.

As the planet warms, the ocean has absorbed as much as 91% of the excess heat that is trapped in the Earth’s atmosphere, according to the National Oceanic and Atmospheric Administration. In 2023 surface temperatures in the North Atlantic reached record levels.

Marine biologists warn that rapid warming trend will make coastal waters less hospitable to the marine life that thrives there now, but more hospitable to many species of harmful algae — and the toxins they sometimes generate.