ST. LOUIS — President Biden’s administration finalized regulations Friday that protect hundreds of thousands of small streams, wetlands and other waterways, repealing a Trump-era rule that federal courts had thrown out and that environmentalists said left waterways vulnerable to pollution.

The rule defines which U.S. waters are protected by the Clean Water Act. For decades, the term “waters of the United States” has been a point of contention between environmental organizations, which want to broaden limits on pollution entering the nation’s waters, and farmers, builders and industry groups that say extending regulations too far is onerous for business.

The Environmental Protection Agency and the Department of the Army say the reworked rule is based on definitions that were in place before 2015. Federal officials said at the time that they’d written a “durable definition” of waterways to reduce uncertainty.

In recent years, however, there has been a lot of uncertainty. After the Obama administration sought to expand federal protections, the Trump administration rolled them back as part of its unwinding of hundreds of environmental and public health regulations. A federal judge rejected that effort. And a separate case is being considered by the Supreme Court that could yet upend the finalized rule.

“We have put forward a rule that’s clear, it’s durable, and it balances ... protecting of our water resources with the needs of all water users, whether it’s farmers, ranchers, industry, watershed organizations,” Radhika Fox, assistant EPA administrator for water, told the Associated Press.

The new rule is built on a pre-2015 definition, but is more streamlined and includes updates to reflect court opinions, scientific understanding and decades of experience, Fox said. The final rule will modestly increase protections for some streams, wetlands, lakes and ponds, she said.

The Trump-era rule, finalized in 2020, had long been sought by builders, oil and gas developers, farmers and others who complained about what they said was federal overreach into gullies, creeks and ravines on farmland and other private property.

Environmental groups and public health advocates countered that the Trump rule allowed businesses to dump pollutants into unprotected waterways and fill in some wetlands, threatening public water supplies downstream and harming wildlife and habitat.

“Today, the Biden administration restored needed clean water protections so that our nation’s waters are guarded against pollution for fishing, swimming and as sources of drinking water,” said Kelly Moser, senior attorney for the Southern Environmental Law Center’s Clean Water Defense Initiative.

Jon Devine, director of federal water policy for the Natural Resources Defense Council, called repealing the Trump-era rule a “smart move” that “comes at a time when we’re seeing unprecedented attacks on federal clean water protections by polluters and their allies.”

But Sen. Shelley Moore Capito (R-W.Va.) said the rule is “regulatory overreach” that will “unfairly burden America’s farmers, ranchers, miners, infrastructure builders and landowners.”

Jerry Konter, chairman of the National Assn. of Home Builders, said the new rule does not clarify whether the federal government will regulate water in places such as roadside ditches and isolated ponds.

A 2021 review by the Biden administration found that the Trump rule allowed more than 300 projects to proceed without the federal permits required under the Obama-era rule, and that the Trump rule significantly curtailed clean water protections in states including New Mexico and Arizona.

In August 2021, a federal judge threw out the Trump-era rule and reinstated a 1986 standard that was broader in scope than the Trump rule but narrower than the Obama administration’s. U.S. District Judge Rosemary Marquez in Arizona, appointed under President Obama, said the Trump-era EPA had ignored its own findings that small waterways can affect the well-being of the larger waterways they flow into.

Meanwhile, the Supreme Court is considering arguments from an Idaho couple backed by business in their push to curtail the Clean Water Act. Chantell and Michael Sackett wanted to build a home near a lake, but the EPA stopped their work in 2007, saying that wetlands on their property were federally regulated and that they would need a permit.

The case was heard in October and tests part of the rule the Biden administration carried over into its new version.

Now-retired Justice Anthony M. Kennedy wrote in 2006 that if wetlands “significantly affect the chemical, physical, and biological integrity” of nearby navigable waters such as rivers, the Clean Water Act’s protections apply. The EPA’s rule includes this test. Four conservative justices in the 2006 case, however, said that federal regulation applied only if there was a continuous surface connection between wetlands and an obviously regulated body of water such as a river.

Charles Yates, an attorney for the libertarian Pacific Legal Foundation, said the new rule shows the importance of the Supreme Court case since the definition of U.S. waters “shifts with each new presidential administration.”

“Absent definitive guidance from the Supreme Court, a lawful, workable, and durable definition of ‘navigable waters’ will remain elusive,” he said in a statement.

The Biden rule applies federal protections to wetlands, tributaries and other waters that have a significant connection to navigable waters, or if wetlands are “relatively permanent.”

The rule sets no specific distance for when adjacent wetlands are protected, but says several factors can determine whether a wetland and a waterway can affect the other’s water quality and quantity. It states that the effect “depends on regional variations in climate, landscape, and geomorphology.”

For example, the rule notes that in the West, which typically gets less rain and has higher rates of evaporation, wetlands may need to be close to a waterway to be considered adjacent. In places where the waterway is wide and the topography flat, “wetlands are likely to be determined to be reasonably close where they are a few hundred feet from the tributary,” the rule states.

Fox said the rule wasn’t written to stop development or prevent farming.

“It is about making sure we have development happening,” she said, “that we’re growing food and fuel for our country but doing it in a way that also protects our nation’s water.”

Salter and Phillis write for the Associated Press.