They remove algae, nitrogen and chemicals from the water.
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"Mother Nature had a plan. She had a system. Our problem is we messed with Mother Nature's system," Governor Andrew Cuomo said.
Pollution around Long Island has decimated the clam and oyster populations, meaning dirtier water.
"We know that water is everything to us here on this island. It is our quality of life. It is our heritage. It's our recreation. It is our economy," said Steve Bellone, Suffolk County Executive.
That's why the state is investing $10.4 million to create several shellfish sanctuaries around Long Island.
It's the largest shellfish restoration project in the country.
"It's going to not only use the shellfish to filter the water, but also put them out in the way that the population will reproduce naturally," said Chris Gobler, Stony Brook University.
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The shellfish sanctuaries will be located in South Oyster Bay, Hempstead Bay, Huntington Harbor, Bellport Bay and Shinnecock Bay.
"So basically we have the hatchery that produces the shellfish, then they go out to the 69 nursery sites and then they get concentrated back down to five sanctuary sites," said Chris Pickerell, Cornell Cooperative Extension.
The sites will be closely monitored by the DEC and local law enforcement.
Anyone caught harvesting the shellfish will face large fines.
"These sanctuaries will be clearly marked with special buoys. There's obviously commercial harvesting. This is not a place where you should commercially harvest," Gov. Cuomo said.
The shellfish will be put in the water in November of 2018. The sites will be monitored by local environmental officials.