EAST ROCKAWAY, N.Y. » The water flowing out of the Bay Park sewage plant here in Nassau County is a greenish-gray soup of partially treated human waste — a sign of an environmental and public health disaster that officials say will be one of the most enduring and expensive effects of Hurricane Sandy.

In the month since the storm, hundreds of millions of gallons of raw and partially treated sewage from crippled treatment plants have flowed into waterways in New York and New Jersey, exposing flaws in the region’s wastewater infrastructure that could take several years and billions of dollars to fix.

In New York alone, Gov. Andrew M. Cuomo has estimated that $1.06 billion will be needed just for repairs to treatment plants. But authorities now acknowledge that they will have to do far more.

Motors and electrical equipment must be raised above new flood levels, and circuitry must be made waterproof. Dams and levees may have to be built at some treatment plants to keep the rising waters at bay, experts say.

Failure to do so could leave large swaths of the population vulnerable to public health and environmental hazards in future storms, experts said.

"You’re looking at significant expenditures of money to make the plants more secure," said John Cameron, an engineer specializing in wastewater treatment facilities who is chairman of the Long Island Regional Planning Council. "There is no Band-Aid for this," Cameron said. "This is the new normal."

At least six sewage plants in the New York region shut down completely during the storm, and many more were crippled by storm surges that swamped motors and caused short circuits in electrical equipment.

In New Jersey, workers at the Passaic Valley Sewerage Commission plant, the fifth-largest facility in the country, had to evacuate as floodwaters surged in and wastewater gushed out.

The Middlesex County Utility Authority plant in Sayreville, N.J., pumped about 75 million gallons of raw sewage a day into Raritan Bay for nearly a week before power was restored, said Larry Ragonese, a spokesman for the New Jersey Department of Environmental Protection.

Operations at both plants have yet to be fully restored.

Bay Park, a sprawling complex off Hewlett Bay near the New York City border, serves 40 percent of Nassau County.

When Hurricane Sandy arrived, its force blindsided workers. They had spent days shoring up the facility with emergency measures but did not anticipate the surge.

In less than 30 minutes, engines for the plant’s main pumping system were under 12 feet of water, and sewage began to back up and overflow into homes. In one low-lying neighborhood, a plume of feces and wastewater burst through the street like a geyser.

The plant shut down for more than 50 hours, and about 200 million gallons of raw sewage flowed into channels and waterways.

"Never ever, ever has this happened before," said Michael Martino, a spokesman for the Nassau County Department of Public Works.

On Thursday, Martino said that the plant was now fully operational and that the treatment of sewage was improving day by day.

Two other plants on Long Island, in Lawrence and Long Beach, were also crippled.

And the Rockaway Wastewater Treatment Plant in Queens had significant damage. Others, including the Cedar Creek Water Pollution Control Plant, which serves another 40 percent of Nassau County, and Bergen Point, another large plant in Suffolk County, escaped relatively unscathed.

Still, even those plants may not fare so well in the future, said Cameron of the Long Island Regional Planning Council.

Almost all facilities in the region are situated close to sea level and are vulnerable to storm surges, he said. Many were built decades ago, when populations were smaller and weather less inclement.

Even before Hurricane Sandy, the Bay Park plant in Nassau County needed new equipment.

When it was completed in 1949, the population of Nassau County was half what it is today. The plant now serves 550,000 residents and has struggled to keep pace with demand.

During heavy rains, there are occasional sewage leaks, particularly in low-lying areas, residents say. Last year, the county was fined $1.5 million for, among other violations, illegally pumping about 3.5 million gallons of partially treated sewage into East Rockaway Channel.

For the residents of Barnes Avenue in Baldwin, a low-lying stretch about three miles from the Bay Park plant, the failure during Hurricane Sandy was the culmination of their worst fears, though hardly a surprise.

They said they had long complained to Nassau County about sewage that flooded streets and occasionally homes during heavy rains. After Tropical Storm Irene sent human waste splashing onto lawns and front porches, residents said, the county bolted manhole covers shut to prevent them from opening.

During Hurricane Sandy, the manhole covers stayed in place, but the force of wastewater rushing up through the ground around them washed away part of the road.

"With Sandy it was, I hate the cliche, the perfect storm," said John Malinowski, 54, a graphic designer who lives with his wife in a two-story home on Barnes Avenue. "When Bay Park failed and they couldn’t get the sewage out of the system, that’s when this became a real catastrophic event here."

On a visit this week, the smell of excrement still hung over the tidy neighborhood as workers in white hazmat suits attempted to decontaminate homes. Sewage, mixed with four- to five-foot-high floodwaters, infiltrated floors and walls, and many homes must be stripped to their wooden frames to be fully decontaminated. Some may not be salvageable.

Elsewhere, officials are still evaluating the environmental impact of leakages.

In the Raritan Bay, the Hudson River, and the waters around the Bay Park plant, the Environmental Protection Agency has detected dangerous levels of fecal coliform, a bacteria associated with human waste, and has urged people to avoid contact with the water. Bans on shell fish have been imposed in some regions.

Eventually the tides will flush much of the wastewater into the Atlantic Ocean where it will break down. There is concern though, that some contamination could go into the sentiment and be buried, particularly around Bay Park, where the waters are flushed out more slowly.

"This is the largest sewage release in the history of Long Island," said Adrienne Esposito, executive director of Citizens Campaign for the Environment, an advocacy group. "This brings to a new level the public health threat and the duration for the contamination, which will have a serious adverse impact on our beaches and our bays."

© 2012 The New York Times Company