"What's in the water clearly affects what's in the air," said Eli Dueker, a postdoctoral researcher at Columbia University's Lamont-Doherty Earth Observatory, who conducted the study.
"The transfer of contamination we have found at Newtown Creek could be happening in any place where the water is heavily polluted."
The pollution is being caused by an aeration process to release the toxins from the waterway, which has been declared a Superfund site.
The city's Department of Environmental Protection is responsible for the cleanup.
The report said that more information must be gathered to determine if the air pollution is creating a health risk.
The study, which showed the same kind of bacteria in the air as in the creek which has been polluted by decades of oil spills and sewage dumps, is the first to find such a link between air and water pollution, the researchers said.