New York (CNN Business) The New York Harbor for years has been polluted and depleted of marine life. But one nonprofit is working to clean the murky water and revive its long-lost ecosystem — one oyster at a time.

The Billion Oyster Project has worked since 2014 to rebuild oyster reefs in the waters surrounding New York City. The creatures are natural purifiers: A single adult oyster can cleanse about 50 gallons of water per day. And their reefs can provide a habitat for other marine life and help protect New York's shores against storm surge during rough weather.

The group has so far restored about 30 million oysters to local waters. But that's still a tiny fraction of what used to thrive in the area.

"Without the oyster reefs, the whole shoreline is fundamentally changed," the group's executive director, Pete Malinowski, told CNN Business' Rachel Crane. "We think oyster reefs can be part of an integrated approach to resiliency and proactive planning for climate change."

Malinowski said his team is seeing promising signs. Last year, there was a "dramatic" increase in the number of wild oysters that latched on to Billion Oyster Projects' reefs.

"For restoration to be successful, you need the recruitment of wild oysters from the system," Malinowski said. It could help the population grow exponentially.

Like the group's name implies, it hopes to one day return one billion oysters to New York's waterways.

How it works

Billion Oyster Project partners with more than 70 restaurants in New York City. The businesses save up their oyster shells rather than tossing them, and a collection partner for the Billion Oyster Project rounds them up and carts them off to Governors Island, a small island due east of the Statue of Liberty.

The shells are then left outside for at least a year. This allows the elements to naturally cleanse them of organic matter before they are sent to the the New York Harbor School, a maritime-focused public high school on Governors Island, which is heavily involved in the project.

Students grow and hatch baby oysters that are then attached to the cleaned shells. The shells and larvae are grouped together and strategically placed somewhere off New York's coastline.

Billion Oyster Project has started twelve reefs so far, some close to shore, and others out in deeper waters.

Engaging the community — particularly young students — throughout the process is a top priority. The group works with more than 75 public schools across all five New York City boroughs, and students take field trips out to reef sites or research station to learn how to measure water quality and track oyster growth.

"Our work with schools and communities gets people down to the water's edge and starts to reestablish the relationship that New Yorkers used to have with the ecosystem," Malinowski said.

Billion Oyster Project is funded through a variety of grants from state and city backers. The National Science Foundation also recently renewed support for the project, offering a two-year $4.5 million grant.

The Big Oyster

Hundreds of years ago, New York Harbor teemed with more than 200,000 acres of live oyster reefs. The molluscs cleaned and filtered the water, naturally removing pollutants. Dolphins, seals and other creatures, drawn to the vibrant ecosystem, swam just off the shore of Manhattan.

"When Europeans first arrived in New York Harbor, there were oyster reefs everywhere and there were so many fish that they couldn't physically get out of the way of the boats," Malinowski said. "In about 100 years, we had harvested all the native oysters from the harbor. All those oysters were eaten, consumed locally by New Yorkers, and shipped all over the world as food."

Oysters were a favorite treat among New York City's skyrocketing population in the 19th century. Street vendors and restaurants began to hawk the cheap, salty seafood.

By the 1900s, New York Harbor was polluted and practically lifeless. It wasn't until 1972, with the passage of the Clean Water Act, that the law prohibited dumping waste or raw sewage into the harbor.

Only recently has the water become clean enough to support shellfish like mussels, oysters and clams.

Storm Surge

Water purity is not the only reason New York's waters suffered without oysters. For centuries, their large reefs served as natural breakwaters — underwater barriers that help protect land from storm surge and erosive waves — around New York's coastline.

Those reefs were long gone by the time Hurricane Sandy ripped through the state in 2012, and experts have suggested the lack of oyster reefs and other natural barriers exacerbated the damage.

The Billion Oyster Project's work could slowly rebuild the breakwaters. But,"the oyster reefs that protected New York City before they were removed ... took hundreds of years to grow to the size that they needed to be to protect the shore," Malinowski said.

Instead of waiting for a full-grown oyster reef to begin mitigating storm surge, The Billion Oyster project is partnering with another group, Living Breakwaters, to create artificial reefs across two miles of Staten Island shoreline. Oysters can then build reefs around the structures, making it larger and sturdier.

The Living Breakwaters initiative, which is due to begin construction this year, is funded in part by a $60 million disaster recovery grant awarded by the federal Department of Housing and Urban Development in 2013.

Kate Orff, who founded Scape, the design firm that is spearheading the project, said it is past time for New Yorkers to start taking serious steps to combat the impact of climate change — which is expected to bring increasingly volatile weather and higher sea levels.

"We need to drastically look at landscape strategies," she said.

What's ahead for BOP

Billion Oyster Project isn't the first initiative of its kind.

The Oyster Recovery Partnership was launched in 1994 to help reestablish oyster populations off the coast of Virginia and Maryland.

A large chunk of the oyster population there has been restored. And the group encourages other localities to take on similar measures.

Malinowski, the Billion Oyster Project executive director, said he hopes more initiatives will pop up as people begin to realize the crucial role oysters play in keeping oceans healthy.

But there's still a long way to go before the oyster population near New York is anywhere near pre-industrialization levels.

The project's progress is "exciting and it's validating in a big way — but it's also sobering because there's a long way to go," he said.

Malinowski said he is heartened by the participation of local grade schoolers. He said he hopes the work will inspire younger generations to consider environmental and ecological issues no matter what they do.

"People in New York will become more and more aware that the reason [New York Harbor is] polluted is because it's contaminated with human waste, that's it's full of trash and plastic," he said. "You can just imagine walking to Central Park in the afternoon on a Saturday and having the gates closed because it was full of human waste and trash."

"New Yorkers wouldn't stand for that and it would stop."