Thomas Burke, a professor and associate dean at Johns Hopkins School of Public Health, said the Gowanus and Newtown Creek—whose cleanups haven't begun in earnest yet—are more vulnerable to flooding risks than sites in more advanced stages of remediation, where caps and liners have already been placed over bottom-lying toxic material.

"There really has to be a careful evaluation of whether there has been any disturbing of the waste," Mr. Burke, a former director of sciences and research at the New Jersey Department of Environmental Protection, said. "Flooding moves things around much more quickly."

Hurricane Katrina in 2005 doesn't offer any clear-cut lessons. During Katrina, several Superfund sites in Louisiana flooded, including the Agriculture Street Landfill Superfund site, which was used to burn debris after Hurricane Betsy hit New Orleans in 1965. In the 1970s and 1980s, a residential development, elementary school and playground were placed atop the site. After Katrina's passage, workers found high levels of cancer-causing hydrocarbons in the courtyard of an apartment complex on the site littered with residential debris. But the ground there hadn't been disturbed by the floodwaters, says Tom Harris, administrator for the remediation division of the Louisiana Department of Environmental Quality. "We never really figured out what the heck was going on," he says.

Ground-water sample tests by the EPA also showed elevated levels of arsenic and other metals at two other sites, the Delatte Metals Superfund Site in Tangipahoa Parish and the PAB Oil Superfund Site in Abbeville, La., according to the EPA's website.

New Jersey officials downplayed any problems. "There was no major flooding in North Jersey. Superfund sites were not inundated by tidal surges," said Larry Ragonese, a spokesman for the state environmental agency.