While scientists have been performing extensive studies for more than a decade, no one can explain what is killing Shinnecock Bay, a once-productive shellfishing area on the East End that runs from Quogue to Southampton.
The 9,000-acre Shinnecock Bay shares many of the problems that affect other Long Island bays and lakes: too many cesspools pouring nutrients and pollutants into the underground water supply; poor flushing action that fails to bring in enough fresh ocean water each day; high levels of phosphates and pesticides; and pollutants from road runoff.
Yet none of those things -- alone or acting together -- can explain precisely why clams and other shellfish fail to breed in so much of the bay, or why three distinctly different species of algae bloom at different times, or even why -- in the highly polluted western part of the bay -- clams that are 10 or 20 years old grow big and thick, but tiny seed clams suffer a 90 percent mortality rate.
"We're always trying to figure out what we can do to make the waters healthier and more productive," Southampton Town trustee Fred Havemeyer said. "It's really an uphill battle."
But now, in an ambitious $3 million experiment, Stony Brook University's School of Marine and Atmospheric Sciences recently started a five-year project designed to do what others have not -- bring Shinnecock Bay back to health.
Most of the work will be done by the same clams and oysters that have been harvested from Long Island's bays since before Colonists settled here in 1640. Those shellfish are actually tiny treatment plants, sucking in water and filtering out the nutrients they need to grow, then putting out clearer water.
But they have to go in parts of the bay still healthy enough to support their growth, and they must inhabit areas where they will not be taken out by the baymen who earn their living from clamming.
That requires Southampton's five trustees -- who have absolute control over the bay bottom -- to create a series of sanctuaries in the bay where clamming will be prohibited, and where the clams and oysters can reproduce and increase the biological filtering.
Scientists will also plant more eel grass to encourage shellfish growth and soak up pollutants, and will harvest seaweed to remove some nutrients and discourage algae blooms.
The work could also include the Shinnecock Nation, which has a shellfish hatchery. Scientists have been holding preliminary talks about buying some of the clams they plan to put into the bay from the tribe.
Stony Brook scientist Christopher Gobler is one of the key researchers on the project.
He said that while a lot is known about Shinnecock Bay, there is still much more to learn.
"We actually have a lot less data on Shinnecock Bay than the other bays," he said. "Every year, we have three different algae blooms in this system. That's unprecedented."