Facing a chronic problem of raw sewage emptying into city waterways during rainfalls, and struggling to meet health regulations, New York City environmental officials are turning to a new method of treating bacteria in sewage: dumping chlorine into sewer pipes leading to the waterways.

The city’s Department of Environmental Protection has long tried to mitigate the pollution and health risks from the estimated 20 billion gallons per year of untreated sewage that flow into city waterways when treatment systems are overwhelmed during a rainfall.

In recent years, the city has promoted projects like new retention tanks and has planted patches of greenery to lessen the runoff during rainstorms.

But some environmental advocates claim that details have been scant on the city’s plan to disinfect wastewater by chlorinating it inside pipes just before the waste discharges into three bodies of water in Queens and the Bronx.

“They’re using the most worrisome and unproven technique that we have in our toolbox,” said Sean Dixon, a staff lawyer at Riverkeeper, a group that seeks to protect the Hudson River and its tributaries. “It’s like they’re grabbing the last straw and using the cheapest and least effective method.”

In response to this and other water-quality concerns, a coalition of local environmental groups announced recently that they intended to sue the United States Environmental Protection Agency, saying the agency had not adequately protected water quality in New York City’s waterways under the federal Clean Water Act.

Federal officials said they would not comment on the allegations and directed questions regarding the chlorination to New York State’s Department of Environmental Conservation, which is responsible for enforcing federal regulations and standards that the city must follow.

Discharge from the sewer system in Brooklyn. A New York City plan to add chlorine to some sewage pipes in Queens and the Bronx is meant to disinfect wastewater, but floating debris would remain. Credit Yana Paskova for The New York Times

The city’s plan includes locations and budgets for chlorination facilities to be built to serve three waterways: Alley Creek and Flushing Creek in Queens and the Hutchinson River in the Bronx.

Chlorination is commonly done in the more controlled setting of wastewater treatment plants, rather than in sewer pipes flowing directly into waterways.

Advocates called the chlorination plan, while comparatively small in such a vast sewage system, an unusual initiative that they worry might be expanded to other areas of the city. They cited a separate pilot program that the city has underway to add chlorination to a sewer pipe in Spring Creek, a neighborhood in Brooklyn.

A spokesman for the city’s Department of Environmental Protection, Ted Timbers, said there were currently no other approved plans that included chlorination in sewer pipes.

Mr. Timbers said that the chlorination would run from May through October and that the sewage would undergo a dechlorination process before being discharged into the waterways.

He called chlorine “the most widely used disinfectant for water and wastewater treatment in the U.S.” and said the plan had been discussed with the public at neighborhood meetings.

And, Mr. Timbers said, “New York Harbor is cleaner and healthier today than it has been in more than a century.”

Newtown Creek in Brooklyn. Sewage can bypass treatment plants on rainy days when output from residences and businesses and water runoff push the processing systems beyond its limits. Credit Yana Paskova for The New York Times

Sean Mahar, a spokesman for the state’s Department of Environmental Conservation, said the state would continue to hold the city’s Department of Environmental Protection accountable “for extensive monitoring” and press it “to routinely report data to the state to ensure compliance with our strict standards to protect public health and the environment.”

Much of the advocates’ outrage was spurred by plans released last month outlining how the city aimed to address sewer overflow in the years to come.

Larry Levine, a senior lawyer with the Natural Resources Defense Council, faulted the plans for failing to call for major reductions in untreated wastewater outflow, describing it as an example of city and state officials failing to meet federal health standards.

As the city’s population increases, much of its sewer system remains antiquated, and updating it is complicated and expensive. City officials say the system treats about 1.3 billion gallons of city wastewater on a dry day and can handle twice that amount during moderate rainfall.

But because most of the city’s 305 square miles are impenetrable surfaces like rooftops, roadways and playgrounds — city officials estimate 72 percent — torrents of runoff rainwater flood storm drains and sewers that also handle output from sinks and bathrooms in homes and businesses.

When this combination is beyond the capacity that a local treatment plant can handle, the excess bypasses processing plants to avoid backing up the systems and flows untreated into the city’s waterways, often causing pathogen levels to rise.

The city has managed to drastically improve water quality in recent decades, turning many dismal waterways into spots that are now swimmable and brimming with aquatic life.

Newtown Creek. As New York City’s population increases, much of its sewer system remains antiquated, and updating it is complicated and expensive. Credit Yana Paskova for The New York Times

Mr. Timbers said New York City had the largest environmentally sustainable infrastructure program in the country and had invested significant amounts of money to build retention tanks and curbside gardens to reduce runoff into sewers.

The city has a long-range plan to invest $1.5 billion by 2030 on environmentally sustainable infrastructure and has over the last decade invested more than $10 billion to upgrade wastewater treatment plants and improve water quality. In January, the city agency announced that nitrogen levels had declined in city waterways as a result of $1 billion in upgrades at four wastewater treatment plants.

The agency also plans on building a 25-million-gallon storage tunnel — estimated to cost at least $1.2 billion — to reduce outflow into Flushing Bay.

Mr. Dixon, of Riverkeeper, hailed those projects but called some strategies shortsighted, such as the chlorination of sewage in pipes, which he said often failed to completely disinfect the material and did not treat certain toxins in the runoff. In addition, Mr. Dixon said, residual chlorine can devastate marine life and hinder water quality testing.

Timothy Eaton, a hydrologist at the School of Earth and Environmental Sciences at Queens College, said that while chlorine was an effective disinfectant in controlled settings like swimming pools, using it in outflowing sewer pipes was “a very different ballgame.” Unpredictable and constant changes in the volume of sewage flow can complicate the dechlorination process by creating uncertain dosages and residual chlorine, he said.

“It’s very difficult to predict the amount of water you’re going to get at any period of time,” he said. “If you overdose it, you’re basically treating Flushing Creek and Flushing Bay like swimming pools.”

The chlorination plan would not remove floating debris or prevent oxygen depletion in the outflow, said Mr. Eaton, who with another hydrologist at the school, Gregory O’Mullan, has spoken out against the chlorination.

Mr. O’Mullan called it a “Band-Aid” treatment that gives the chlorine limited contact time to disinfect.

“This is low-level treatment,” he said, adding that it was the kind of approach that would have been used decades ago.