HARRISBURG — State environmental regulators have agreed to take more precautions before they approve certain permits for oil and natural-gas drilling sites where well construction poses a pollution threat to some of Pennsylvania’s highest-quality waterways.

The state Department of Environmental Protection agreed to the measures to settle a complaint by the Chesapeake Bay Foundation first filed in 2009 that also asserted the agency had approved three deficient permit applications.

The settlement, dated Wednesday, essentially reverses some steps the department took two years ago to speed up the permitting process for Pennsylvania’s booming natural gas industry. The foundation argued the speedup was illegal.

Primarily, the agreement will impact drilling-related activity — land clearing, production, processing, treatment and pipeline construction — in northern Pennsylvania, where the state’s “high quality” and “exceptional value” waterways are predominantly found, said foundation scientist Harry Campbell.

“The heart of the matter is that those water bodies overlay, almost to a T, where predominantly the drilling activity is occurring,” Campbell said. The settlement contains “very significant sea changes in the way we are permitting those facilities within those watersheds that house the very special water.”

The settlement was approved by an Environmental Hearing Board judge and included subsidiaries of Houston-based Ultra Petroleum and Calgary-based Talisman Energy. The resulting stricter review process could take up to 60 days. Currently, those permits can get approved in a matter of two weeks.

“It’s important to give the DEP more time to look at everything,” foundation lawyer Amy McDonnell said. The DEP said in a statement that the revisions would make the permit review process “more robust.”

“This proposed settlement is an important step forward in our continued commitment to oversee this industry in an environmentally and economically conscious manner,” the statement said.

The agency must still take public comment for 60 days on the proposed change.

Under it, the department will require the stricter review if drilling-related activity poses the potential to pollute a high-quality waterway, or if a well pad is on a flood plain.