Rebuilding An Ecosystem

Pictured Above: Stony Brook researchers set oysters on the man-made reefs in Shinnecock Bay | ShiRP photo

Like many water bodies across Long Island, the ecosystem of Shinnecock Bay, which sits between Hampton Bays, Quogue and Westhampton and the barrier beaches of Dune Road, was in serious decline a decade ago, but unlike those other water bodies, that decline has begun to reverse.

Scientists at Stony Brook University’s School of Marine and Atmospheric Sciences (SoMAS) believe they know why things are improving: Because of the restoration work they’ve spent the past ten years doing.

Like many of the South Shore’s estuaries, the shallow waters and lack of tidal movement in an area adjacent to some of the most heavily developed residential land on Long Island has proven over the 20th Century and into the first decade of the 21st Century to be a toxic combination, with harmful algae blooms and low oxygen levels in the water setting off a chain of events that causes damage further and further up the food chain. 

By 2011, hard clam landings in Shinnecock Bay had declined more than 99 percent since their peak in 1970, said Dr. Christopher Gobler, chair of Coastal Ecology and Conservation at SoMAS, in a May 6 Zoom seminar on the heath of Shinnecock Bay. Similar patterns were seen in other South Shore estuaries, including Moriches Bay and the Great South Bay, which has seen a near-total collapse of its once thriving clam industry.

But last year, 2020, was the “best hard clam harvest in Shinnecock Bay in over 35 years,” said Dr. Gobler. “It was at levels that haven’t been seen since the onset of the brown tide in 1986.”

“It’s the only system where landings are increasing,” he added. “In Moriches Bay, landings are down 61 percent. The script has been flipped. In the 1970s, only four percent of hard clam landings were coming out of Shinnecock Bay. Now they’re accounting for 44 percent of the landings from South Shore estuaries. The Great South Bay is 32 percent, but Shinnecock Bay is one-tenth the size of the Great South Bay.”

Christina Woodward and Jennifer Katz, two Stony Brook University undergraduates, helped deploy more than 129,000 oysters this spring, as part of a program that has planted more than three million oysters in spawner sanctuaries in the estuary | ShiRP photo

So how did this happen?

After seven years researching the conditions in Shinnecock Bay, SoMAS researchers, partnering with the community and other ecologists, began implementing a plan to create spawner sanctuaries for hard clams in the western part of the bay, foster eelgrass beds in areas of the estuary they’d be most likely to thrive, and creating six oyster reefs throughout the bay, which provide both natural habitat for marine creatures and filter a staggering amount of sea water.

They called the effort the Shinnecock Bay Restoration Program (ShiRP).

Based on successful work done by Cornell Cooperative Extension reseeding scallops in Orient, researchers created two so-called “spawner sanctuaries” on the northwest side of Shinnecock Bay, areas where the Southampton Town Trustees have prohibited the harvest of clams, while researchers seeded the area with more than three million hard clam larvae. While clammers were unable to take clams from these areas, the theory was that a stable and thriving population of spawning clams here would help repopulate the entire estuary. 

“That was the easy work. Next was understanding how these clams are doing,” said Dr. Gobler.

The data was astounding. 

“Hard clam landings have increased 1,000 percent since we began this program,” he said. “And when you look at the sizes of clams being harvested, the biggest increase is littleneck clams, a 1,771 percent increase…. This tells us these are new clams that are only a few years old, three to four years. That means they all were produced since the beginning of the ShiRP program, and over time have become the majority of the harvest.”

The oyster reef project has been “more of an experimental approach,” said Dr. Gobler, who added that Shinnecock Bay was much better known as a habitat for hard clams than oysters.

With permits from the New York State Department of Environmental Conservation, Stony Brook researchers built six oyster reefs in the western portion of the bay, using bags filled with oyster shells on which living oysters were set atop the shells. In all, the reefs were initially comprised of about 3 million living oysters.

Oysters grow very quickly, and while these reefs were all installed in the past three to four years, some of the oysters in the reefs are now as much as seven to eight inches long. 

The reefs are now providing habitat for grass shrimp, mud crabs, and oyster toadfish, which, living up to their name, “really do like oyster reefs,” said Dr. Gobler.

It’s an oft-cited fact that an oyster can filter up to 50 gallons of water per day, and in a bay that had long been plagued by harmful algae blooms, the scientists were happy to see the oysters filtering the water. Dr. Gobler said that it’s important to remember that, while oysters are filtering the water the fastest, the clams are also filtering seawater.

“We’ve had four years without a brown tide bloom. That hadn’t happened since 1981 in Shinnecock Bay,” said Dr. Gobler.

At the beginning of the ShiRP program, the western portion of the bay had also been closed to shellfishing due to the toxic red algae Alexandrium in three out of five years. There have been no shellfishing closures due to Alexandrium in the past two years, said Dr. Gobler, and rust tide, another harmful algae bloom, “we have not seen since 2017.”

Another area of successful ecosystem restoration in the bays has been eelgrass restoration, said Dr. Bradley Peterson, who is working on the eelgrass project. A key to that project has been measuring to find the areas of the bay with high enough water clarity for eelgrass to thrive.

Using a technique pioneered by Chris Pickerell of Cornell Cooperative Extension’s marine center in Southold, researchers set out seed buoys, bags of eelgrass seeds tied to a float, which let the seeds naturally fall out of the bags, along with hand-broadcasting of eelgrass seeds.

“The plant itself has a great ability to claim space when the habitat is good for it,” said Dr. Peterson. “Sediment or algae blooms affect the light, so we needed to predict where light levels are appropriate for grass. Light levels change over the course of the growing season, and we’re most concerned about August, when the plant needs to get enough carbon to be sustained in high temperature environments.”

By sowing seeds in the most conducive areas, Dr. Peterson said, in the eastern portion of the bays, over a six-year period, eelgrass beds “went from less than 8 percent coverage to greater than 43 percent.”

While the western portion of the bay doesn’t have as much eelgrass, Dr. Peterson said that, as the water quality and clarity improves in the western bay due to the clam sanctuaries and the oyster reefs, it will become a better habitat for eelgrass. 

“It’s very telling that the areas with increase in light overlay the hard clam sanctuaries,” he said.

The Suffolk County Department of Health Services, which monitors harmful algae blooms, has also provided evidence of improvements in the bays.

“Chlorophyll levels are progressively decreasing, water clarity is progressively increasing and total nitrogen is declining. Not many places can say that,” said Dr. Gobler.


Beth Young

Beth Young built her first boat out of driftwood tied together with phragmites behind her family’s apartment above the old Mill Creek Inn in Southold. Nowadays, she spends most of her time kayaking, learning about shellfish, writing newspaper stories, trying to sail a Sunfish, and watching the way the bay changes from day to day. You can send her a message at

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