The Biden administration is set to toss out President Donald Trump’s efforts to scale back the number of streams, marshes and other wetlands that fall under federal protection, kicking off a legal and regulatory scuffle over the fate of wetlands and waterways around the country, from the arid West to the swampy South.

Michael Regan, head of the Environmental Protection Agency, said his team determined that the Trump administration’s rollback is “leading to significant environmental degradation.” The EPA and Army Corps of Engineers will craft a new set of protections for waterways that provide habitats for wildlife and safe drinking water for millions of Americans, according to a joint statement.

With the announcement, the Biden administration is wading into a decades-long battle over how far federal officials can go to stop contaminants from entering small streams and other wetlands.

“Communities deserve to have our nation’s waters protected,” said Jaime A. Pinkham, acting assistant secretary of the Army for civil works.

Some Republican lawmakers accused the Biden administration of wanting to return to Obama-era clean-water rules and burden farmers, real estate developers and other businesses with new restrictions on how they can use their land.

“This is a gut punch to Iowans, and I will continue to stand up to onerous regulations the administration may seek to impose on our hard-working families,” said Sen. Joni Ernst (R-Iowa).

In 2015, the Obama administration expanded federal authority to stop or curtail development that could harm a variety of wetlands, streams and ditches that feed into larger bodies of water protected under the Clean Water Act.

Heeding the call of home developers, oil drillers and growers who saw the restrictions as detrimental to their livelihoods, the Trump administration rolled back those Obama-era pollution controls.

But critics, including a panel of independent scientists picked by the Trump administration itself, slammed the move for potentially hastening the destruction of waterways, including “ephemeral” streams that appear only after rainfall and help purify water on its way to larger lakes and rivers that serve as sources of drinking water for millions of Americans. The current lack of protections is particularly notable in desert states such as New Mexico and Arizona, the EPA said.

“The science says those streams and these wetlands are an important part of our clean-water system in the United States and should be protected,” said Tom Kiernan, head of American Rivers, a conservation group.

Now, Regan says he’s trying to strike the delicate balance between conservation and development that both the Trump and Obama administrations failed to reach.

“We’ve learned lessons from both, we’ve seen complexities in both, and we’ve determined both rules did not necessarily listen to the will of the people,” Regan told House lawmakers in April.

The Biden administration’s rulemaking could help stem the staggering loss of wetlands.

Since the end of the Revolutionary War, more than half of the 221 million acres of wetlands in what would become the contiguous United States have been drained, often for farming. The rate of destruction began to wane only in recent decades.

In northwest Ohio, for instance, corn and other crops are grown on a vast tract once known as the Great Black Swamp. Farmers began draining it during the 19th century, and now agricultural runoff flows into Lake Erie and feeds the growth of toxic algae that regularly closes beaches and once forced the city of Toledo to suspend tap water use for about two days.

Bill Stanley, state director of the Nature Conservancy in Ohio, said the Trump administration’s withdrawal of federal protections for what few streams remain to filter nutrient waste from fertilizers could make the lake susceptible to even bigger algae blooms.

“ ‘Nutrients’ doesn’t sound like a bad word,” he said, “but when you get too many of them, it causes major problems for our water quality in Ohio.”

But farmers such as Daryl Lies, who raises hogs and sheep and grows vegetables on 160 acres in central North Dakota, say the Obama-era restrictions on wetland development would have been “painstakingly costly for agriculture.” Those rules, he said, “would have made it a lot harder to have the livestock” near a creek that winds along his farm on its way to the Missouri River.

“Farmers and ranchers are the original environmentalists, I say,” said Lies, who heads the North Dakota Farm Bureau. “We’re not the activists, like we hear across the nation, but we are the real environmentalists. We care about taking care of our land and having it there for the next generation.”

The Trump-era rule eased the path for several construction projects, including a commercial, industrial and residential park along the Savannah River, which forms the border between South Carolina and Georgia.

The RiverPort project came with the promise of jobs in shipping and construction. But wildlife officials at the nearby Savannah National Wildlife Refuge warned in 2010 the proposal “represents a significant threat” to its bottomland hardwoods of gum and maple trees and freshwater marshes that attract migrating waterfowl.

Yet after the Trump administration rolled back the Obama-era rule, more than 200 acres of the wetlands in the project’s footprint fell out of federal oversight, according to the Southern Environmental Law Center, which is suing the EPA over the regulation.

“Every day the rule is in place, we are losing protections for 92 percent of wetlands, waters and streams,” said Kelly Moser, a senior attorney at the Charlottesville-based legal advocacy group, citing the organization’s analysis of the impact of the Trump rule.

In total, the EPA and Army Corps said they are aware of 333 projects that no longer require federal water permits under the Trump rule.

A former regulator from North Carolina, Regan arrived in Washington with a reputation as a consensus builder and has spent much of his first months in office listening to both sides of the debate over water protections. Regan met with Lies and other members of North Dakota’s agriculture and oil industries last week during a trip to Bismarck hosted by Sen. Kevin Cramer (R-N.D.).

“I’m cautiously optimistic that we’ll be able to work with this EPA administrator and that he truly is sincere about getting out and getting input,” Lies said.

With the announcement Wednesday, the Biden administration is kicking off a lengthy rulemaking process. It must first strike down the Trump rule before establishing its own definition for which waterways get federal protection.

Some environmentalists are upset the EPA isn’t moving more quickly to revoke the more forgiving water regulations, which will remain in place until part of the rulemaking process is complete. “Today’s action falls well short of the Biden administration’s commitments to protecting our environment and communities,” said Julian Gonzalez, a water policy lobbyist for Earthjustice.

The fate of the EPA’s effort could ultimately hang in the U.S. Supreme Court.

At the center of the decades-long legal storm over water protections is the Clean Water Act, which bans pollution in “waters of the United States” without a permit. The question of what constitutes such water has been up for debate since the law’s passage in 1972.

In a 2006 decision, Justice Anthony M. Kennedy wrote federal officials could step in when there was a “significant nexus” between smaller and larger bodies of water. The Obama administration wrote its rule around that standard.

But after Kennedy’s retirement and with the Supreme Court taking an even more conservative turn with the appointments of three justices by Trump, it’s unclear what sort of rule could now pass muster.

“That is the $64 million question, isn’t it?” said Patrick Parenteau, a professor of natural resources law at Vermont Law School. “It’s got to be a rule that gets five votes on the Supreme Court, and that’s going to be … difficult.”