A federal judge issued a nationwide injunction Thursday against the Trump administration for delaying the Obama-era Waters of the United States rule, dealing a setback to a key piece of President Trump's deregulatory agenda.

The decision by the U.S. District Court in South Carolina means that the so-called Clean Water Rule is again operative in 26 states where district courts have not halted the regulation.

Former Environmental Protection Agency Administrator Scott Pruitt signed a finalized regulation in February delaying the Waters of the U.S. rule until 2020 to allow the agency to go through a process of rewriting a more modest version of it.

Opponents said EPA avoided the customary 30-day waiting period between the rule's finalization and its effective date, circumventing the Administrative Procedures Act, or APA.

“As administrations change, so do regulatory priorities,” said Judge David Norton, an appointee of George H.W. Bush, in his ruling. “But the requirements of the APA remain the same. The court finds that the government failed to comply with these requirements.”

Molly Block, an EPA spokeswoman, said the agency is reviewing the judge's order.

"EPA and the Army [Corps of Engineers] will review the order as the agencies work to determine next steps," she told the Washington Examiner.

The National Association of Manufacturers, a defendant in the case, said it would appeal the decision.

“The ruling is problematic because it creates a patchwork of states where the WOTUS rule applies and others where it does not," said Peter Tolsdorf, the association's deputy general counsel.

The Southern Environmental Law Center represented nine groups, including Charleston Waterkeeper and the Coastal Conservation League, in filing a lawsuit over the Trump administration's delay of WOTUS.

At the same time, 11 Democratic state attorneys general filed a similar lawsuit in the U.S. District Court for the Southern District of New York.

The Obama administration rule, published in June 2015, intended to clarify which waters and wetlands are protected by the Clean Water Act and are subject to federal regulation by the EPA and the Army Corps of Engineers.

Farmers, ranchers, and developers said the rule violated their property rights, forcing them to protect the streams and tributaries that flow through their land.

The EPA recently sent its draft replacement rule to the White House for review, and it should be made public soon.

Under the proposal, the EPA and the Army Corps would enforce the water regulations under the older, limited definition of waterways, which included primarily large bodies of water like rivers.

This story has been updated since publication.