The Environmental Protection Agency will keep polluters on the hook to clean up “forever chemicals” linked to serious health risks, upholding a major rule despite chemical industry opposition.

The decision, which was announced late Wednesday, came despite an effort by a former industry lawyer, who now holds a top post at the agency, to reverse the regulation.

But Lee Zeldin, the administrator of the E.P.A., elected to uphold the rule, a rare move at an agency that has pursued a broad deregulatory agenda. The agency must still defend the rule in court from industry lawsuits.

“Holding polluters accountable” while protecting the public from the family of chemicals known as PFAS continued to be a challenge for the agency, Mr. Zeldin said in a statement.

Upholding the PFAS regulations has been an exception for the Trump administration, which has moved to weaken dozens of other environmental rules, including limits on pollution from tailpipes and smokestacks, as well as protections for forests and wetlands.

Mr. Zeldin is a former House representative from Long Island, where PFAS chemicals used at military and firefighting training facilities as well as two airports have leached into groundwater and contaminated drinking water supplies.