President Trump will sign an executive order Tuesday directing federal agencies to channel the wisdom of late Supreme Court Justice Antonin Scalia in reconsidering an Obama administration rule that expanded Washington’s jurisdiction over state and local waterways under the Clean Water Act.

A senior White House official said Mr. Trump will sign an order that could result in eventual repeal of former President Barack Obama’s “Waters of the U.S.” executive order, a target of complaints from landowners and businesses.

In an unusual directive, Mr. Trump will order the EPA and the Army Corps of Engineers to consider in particular a 2006 opinion by the late Supreme Court Justice Antonin Scalia, who wrote that the “Waters of the United States” should cover only permanent, standing or continuously flowing bodies of water because, he said, that was the definition of “the waters” in Webster’s Dictionary.

The Trump order will instruct the EPA and the Army Corps to “review and reconsider” the Obama order.

Meanwhile, Attorney General Jeff Sessions will be instructed to hold back on any further litigation in the 6th U.S. Circuit Court of Appeals, where the Obama water rule has been challenged.

Last month, the Supreme Court agreed to hear a case filed by the National Association of Manufacturers on whether challenges to the rule should be heard in federal district or appellate courts.

In 2015, the Obama administration expanded the scope of the Clean Water Act, which gives federal agencies authority over the “waters of the U.S.,” after years of debate over where its authority began and ended.

The administration’s rule won praise from environmental groups but opposition from farmers, ranchers and other landowners, who argued that the definition sowed confusion and heightened the risk of regulatory non-compliance by including minor bodies of water such as small agricultural ditches and ponds.

“The rule defines terms like ‘tributary’ and ‘adjacent’ in ways that make it impossible for farmers and ranchers to know whether the specific ditches, ephemeral drains or low areas on their land will be deemed ‘waters of the U.S.,’” said the American Farm Bureau Federation in a statement.

“But these definitions are broad enough to give regulators (and citizen plaintiffs) plenty of room to assert that such areas are subject to CWA regulation,” said the bureau.

Thirty-one states have challenged the rule in court, accusing the Obama administration of federal overreach, while the House Oversight and Government Reform Committee issued a report in October calling the order “a case study in legal shortcuts, predetermined conclusions, and politically motivated timelines.”

David Strayer, a freshwater ecologist with the Cary Institute of Ecosystem Studies, argued in a Feb. 11 op-ed that scaling back the Obama-era expansion “would allow agriculture to pollute more waters and roll out the red carpet for other polluters.”

“And we would be left paying the price, as the quality of drinking water degrades, beaches close, lakes and rivers fill with algal scums, waterfront businesses and property values suffer, and fish, birds and other wildlife disappear,” said Mr. Strayer in the Albany [N.Y.] Times Union.

• Valerie Richardson contributed to this report.

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