The US will spend billions of dollars in a bid to reduce the pollution and clean up its waterways from the Olympic Games in August.
The government has committed $1 billion to the project.
But the clean-up will be controversial in many US cities, where residents have voiced concerns about the impact on health and the environment.
The Environmental Protection Agency (EPA) will oversee the effort, but it will be run jointly with the federal government.
It is the first time a government agency has stepped into a clean-ups operation, the EPA said in a statement.
The clean-water initiative will cost the US between $50 billion and $100 billion over the next two years, depending on how the clean up proceeds.
The EPA will spend $50bn to clean up polluted water at the Olympic sites, EPA chief Gina McCarthy told a Senate committee in January.
It is unclear how many residents in the US are concerned about the pollution.
In an article for the Atlantic, writer James Harkin said the pollution was likely to affect hundreds of thousands of people in the affected areas.
He said: “There is an expectation among many residents, including those who live near the Olympic facilities, that if they cannot swim to their nearby swimming pools or restaurants, they may be forced to live in isolated areas that will be far from their families and neighbours.”
But a separate study by the US Geological Survey found that the pollution had no measurable impact on the health of fish.
It found that “the overall average pollution level was about 1,400 mg/l (1.5 milligrams per liter) in the Olympic site and 2,200 mg/g (3.7 milligram per gram) in surrounding lakes.”
This level was similar to the levels found in the surrounding Chesapeake Bay.
“It’s not necessarily going to be the same pollution levels that you see in some of the more polluted places in the country,” James Hagan, a US Geological Society scientist, told the New York Times.
“The extent to which pollution will be different is a very complicated issue.
And there are lots of ways in which it might be different.”
The EPA is also expected to pay for the clean water effort in order to ease public pressure to clean the polluted waterways.
On Sunday, the New England Aquarium, which has been heavily criticised for its treatment of animals in its cages, said it had started using a new cleaning system, which it said would help to protect animals from contamination.