The federal agency announced Wednesday it had completed a thorough assessment of the Gowanus, which runs 1.5 miles through a narrow industrial zone near some of Brooklyn's wealthiest neighborhoods.
Its investigation found the canal is contaminated by various metals and toxic chemicals suspected of being carcinogens.
The EPA also warns people who consume fish and crabs caught in the canal are at risk of exposure.
Last year it named the canal a Superfund site, meaning the government can force polluters to pay for its restoration. The cleanup could cost hundreds of millions of dollars.
Mayor Michael Bloomberg worried the Superfund label would scare away developers.