“But a few years ago, the EPA decided that ‘navigable waters’ could mean nearly every puddle or every ditch on a farmer’s land, or everywhere else that they decide,” the president said. “It was a massive power grab.”

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The final outcome of Trump’s order could have tremendous implications for the agricultural, real estate, gravel, sand and ranching sectors, as well as for critical habitats for aquatic species and migratory birds. Still, it could take well over a year for the directive to be carried out. It will likely trigger a fresh round of rulemaking but could also lead to extensive litigation as the agencies seek to redefine federal restrictions on what accounts for 60 percent of the nation’s water bodies.

Outdoor recreation and environmental groups said the new federal protections were essential to safeguard both public drinking water supplies and the terrain that sustains an array of waterfowl, fish and other species.

“Without the Clean Water Rule’s critical protections, innumerable small streams and wetlands that are essential for drinking water supplies, flood protection, and fish and wildlife habitat will be vulnerable to unregulated pollution, dredging and filling,” said Bob Irvin, president of American Rivers.

The push to unravel the rule marks yet another shift in a decades-long debate over to what extent the federal government can dictate activities affecting the wetlands, rivers and streams that feed into major water bodies. The controversy has spurred two separate Supreme Court decisions, as well as a more recent federal appellate court ruling, as the two previous administrations sought to resolve the matter through executive actions.

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Two Supreme Court decisions that came down during the George W. Bush administration, in 2001 and 2006, fostered uncertainty over exactly what falls under the federal jurisdiction under the Clean Water Act. In the 2006 Rapanos v. United States decision, for example, the court’s four most conservative justices at the time offered a very constrained view that only “navigable waters” met this test. But Justice Anthony M. Kennedy, who refused to join either the conservatives or the liberals, suggested in a concurring opinion that the government could intervene when there was a “significant nexus” between large water bodies and smaller, as well as intermittent, ones.

Speaking to reporters Monday, a senior administration official who asked for anonymity in advance of the announcement said the regulation issued in 2015 “vastly expands federal jurisdictions over state waters, and we think . . . it could potentially violate previous Supreme Court decisions.”

While acknowledging that past court decisions have been “confusing,” the official said that administration officials think “the Supreme Court has tried to make it clear that the federal agencies that oversee this issue, the Army Corps of Engineers and the EPA, should be shrinking” their say over smaller bodies of water across the country.

But John Gale, conservation director for Backcountry Hunters & Anglers, who noted that the previous administration had weighed 1 million comments when crafting its rule, said these smaller streams and water bodies create “healthy riparian areas critical to more than 80 percent of our wildlife, including numerous species of big game. Sportsmen will not stand for shortsighted, irresponsible attacks on fundamental conservation laws like the Clean Water Act.”

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The EPA’s most recent administrator, Gina McCarthy, also criticized Trump’s impending order, saying it was the latest example of his administration “sidelining EPA’s public health mission.”

“The only thing these orders do is make clear this Administration will defer needed public health protections for the American people for the sake of partisan politics,” McCarthy said in a statement. “In fact, these EOs reflect the administration’s fear that the court will find the [existing] rules are necessary and legally solid — as EPA has said all along. They can’t change science and facts.”

The rule McCarthy helped oversee has not gone into effect, since the U.S. Court of Appeals for the 6th Circuit put a nationwide stay on the Obama-era rule last year. But opponents of the regulation criticized both the process that led to the regulation, as well as the final product.

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Mace Thornton, a spokesman for the American Farm Bureau Federation, said in an email that as his group has fought against the current policy, “our constant message has been that regulators need to go back to the drawing board to get this rule done right. We welcome this action, but realize a lot of work lies ahead to secure a policy that works in a fair and transparent manner.”

Craig Uden, president of the National Cattlemen’s Beef Association, said in a statement Tuesday that the new administration should treat it the way a rancher would dispose of a farm animal that is no longer useful. “Ultimately, this rule should be taken out behind the barn and put out of its misery,” Uden said.

To further delay the 2015 rule, the senior administration official said, Trump’s executive order will instruct the attorney general to go back to the 6th Circuit and “take appropriate steps to hold that case in abeyance while the evaluation occurs at the Army Corps and the EPA.”

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In addition, the official added, the directive tells the two agencies to “consider thinking about” a decision by Justice Antonin Scalia in 2006 that suggested dramatically curtailing federal jurisdiction over smaller water bodies.

Lowell Rothschild, counsel with the law firm Bracewell LLP, said in an interview that the new administration’s approach “would provide more certainty down the road, but until the rule is completed and the legal challenges to it is complete, that certainty is not going to exist.”

“Whether or not Justice Scalia’s opinion is the correct guidance for interpretation of the Clean Water Act will certainly be litigated,” Rothschild added.