LONG BEACH TOWNSHIP — Southern New Jersey is home to one of the most pristine natural areas on the East Coast — 115,000 acres of protected forest and marsh in Atlantic, Burlington and Ocean counties.

So why is Barnegat Bay, the estuary just north of the Jacques Cousteau National Estuarine Research Reserve, so polluted?

Melanie Reding tried to answer that question Saturday during a lecture at the Long Beach Island Foundation for the Arts & Sciences. Reding spoke on the health of the bay for the group’s  weekly Science Saturday program.

Reding works with the Institute of Marine and Coastal Sciences at Rutgers University, which has been studying that question extensively in the past decade. To get at the answer, she compared Barnegat Bay to the nearby Great Bay at the nexus of the three counties.

People who live on Barnegat Bay know its problems firsthand: a limping shellfish industry, algae blooms that choke the water and a more recent development — stinging jellyfish.

But Great Bay, north of Brigantine, is largely considered a healthy ecosystem.

“Why do we have two systems so close together, but we’re seeing such different things?” she asked.

One reason is natural. Water in Great Bay gets flushed more regularly with the tides into the Atlantic Ocean than water in the shallow Barnegat Bay, which can take as long as 70 days in the summer to circulate completely, she said. As a result, pollution stays in the bay longer.

But there is a manmade culprit, too. The Great Bay is fed from a watershed deep in the heart of the protected Pinelands National Reserve.

“The Mullica Watershed is believed to be the cleanest of any between Boston and North Carolina,” she said.

But the Barnegat Bay watershed shares its creeks and tributaries with strip malls, subdivisions, schools, parking lots and other development. The vast watershed stretches between mile markers 53 and 92 of the Garden State Parkway, covers 38 towns and is home to more than 500,000 people.

Most of the water in the Barnegat Bay estuary begins in creek rivulets that wind like cracked ice through people’s back yards and between shopping centers. These tiny creeks hold 90 percent of the water in the watershed and serve as the prime source of the bay’s pollution, Reding said.

Besides its depleted shellfishery, the Barnegat Bay has seen a rise in plants such as algae and sea lettuce that choke its water. The plants thrive on excess nitrogen — commonly found in fertilizer, acid rain and coal power plant emissions.

The plants block sunlight, killing sea grasses that normally provide a home for fish nurseries, crabs, sea turtles and shellfish. Since 2002, swimmers on Barnegat Bay have had to contend with an abundance of sea nettles, a stinging jellyfish.

Environmental groups and commercial fishermen are trying to reverse decades of pollution in the Barnegat Bay caused by encroaching development. But they are targeting not just the towns with bayfront views but those miles away that are home to the bay’s headwaters. They are trying to persuade mainland residents to curb behaviors that have small but collective effects on the distant bay.

For example, the group Save Barnegat Bay is circulating a model ordinance regulating the use of fertilizer outside homes and businesses. Stafford Township was the first in the area to pass it, but others are examining it, said Rick Bushnell, president of ReClam the Bay, a group that is trying to restore shellfish to the Barnegat Bay.

Bushnell’s group is also reaching out to mainland visitors and schoolchildren who visit Long Beach Island. The lessons visitors learn about the bay will translate into behaviors at home that will help the long-term health of the bay, he said.

“They’ll help us much more up there than they can down here,” he said.

Meanwhile, state voters in November passed an open space referendum. And groups such as the New Jersey Conservation Foundation are buying sensitive land.

Chris Jage, a spokesman with the conservation group, said these land purchases do not help restore damage already done.

“We’re buying up intact ecosystems. It just stops things from getting worse,” he said.

“The biggest environmental challenge is the way we use our land. The uses in the Barnegat Bay watershed crystallized how much our land-use planning affects ecosystems.”

Among the problems identified: overuse of lawn fertilizers and the demands placed on shrinking natural resources, Reding said.

Vivian Grey, an author who spends her summers in Beach Haven, said she plants native species such as beach plum around her home. But many of her neighbors do not think about how their small manicured yards collectively might affect water quality through the excess amounts of fertilizer they require.

“It’s about training the eye about what’s beautiful. For the most part, they’re concerned more about decorating the outside of their own homes than protecting the bay,” she said.

The problems have serious financial implications, commercial clammer Walter L. Johnson said.

“Clamming once was a way of life in the Barnegat Bay. This was once a very productive fishery. Now some aspects of the bay are so retarded, it needs help from the whole system to heal itself,” he said.

Johnson said he liked some of the ideas he heard at the forum Saturday. But he reserved comment about whether the suggestions would work.

“It’s all hope,” he said.

Contact Michael Miller:

609-272-7247