It was not immediately clear which Superfund sites the EPA was referring to.
"It is shameful that President Trump is threatening to abandon these Americans when they most need the federal government's help", said Maryland Rep. Steny Hoyer, the second-ranking House Democrat.
The mayor of San Juan, Puerto Rico, says President Donald Trump's criticism of her hurricane-ravaged country is "unbecoming" of a commander in chief. Some also noted that as the island was reeling from Hurricane Maria, the president was instead tweeting about NFL players' behavior during the national anthem. Puerto Rico has about 24 industrial waste sites contaminated by industries including pesticides and battery recycling.
Only 17 percent of the island has electricity, according to the site.
"After Trump's most recent comments, Cruz responded via Twitter, "@POTUS It is not that you do not get it; you are incapable of fulfilling the moral imperative to help the people of PR. Shame on you!"
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Puerto Rican Governor Ricardo Rossello said on Monday drinking water supplies have been restored to almost 60% of the island but some areas in the north remained at around 20% after Hurricane Maria hit the US territory.
Trump's comments are his latest remarks on Puerto Rico to offer a mix of criticism and support - and to draw what seems to be a direct response from local politicians in the US territory.
The president adds: "We can not keep FEMA, the Military & the First Responders, who have been incredible (under the most hard circumstances) in P.R. forever!" More than a third of Puerto Ricans are still struggling to live without drinking water.
The Environmental Protection Agency is warning Puerto Rico residents not to drink from wells at so-called "Superfund" sites amid reports that some on the island have sought water from the hazardous waste areas.
Officials at the Federal Emergency Management Agency (Fema) say that the government and its partners are only providing 200,000 meals a day to meet the needs of more than 2 million people.