Justice Sonia Sotomayor (June 17, 2015) Photo by Diego M. Radzinschi/THE NATIONAL LAW JOURNAL.

Business groups, 29 states, agricultural organizations and other industries scored a big victory Monday in their long-running challenges to the so-called “Waters of the United States” rule.

The justices in National Association of Manufacturers v. Department of Defense unanimously held that challenges to the Obama-era rule must be filed in federal district courts and not in federal appellate courts.

The 2015 Clean Water rule has been called one of the most consequential regulations ever promulgated under the Clean Water Act. The Trump administration's U.S. Environmental Protection Agency has already announced it plans to repeal the rule and return to the pre-2015 definition of waters of the United States.

Thirty-one states and business and agriculture groups initially challenged the rule in eight appellate and 13 district courts. The U.S. Court of Appeals for the Sixth Circuit earlier imposed a nationwide stay on the rule's implementation after taking jurisdiction over the challenges.

Justice Sonia Sotomayor, writing for a unanimous court Monday, rejected the government's arguments that the judicial review provisions in the Clean Water Act indicated that the challenges belonged in federal appellate court. “Here, Congress' intent is clear from the statutory text,” she said.

With the high court ruling, the Sixth Circuit injunction is no longer effective. “While today's decision may extend the timeline for litigation over the rule, the good news is that it should put the Clean Water Rule back into effect widely, ensuring clear and strong protections for our nation's waters,” said Jon Devine, senior attorney with the Natural Resources Defense Council.

The decision was unsurprising except perhaps in its unanimity, said Schiff Hardin environmental partner Dan Deeb. “The opinion's analysis is predicated upon the Court's reading of the CWA's plain language and underlying legislative intent [of the act's section giving federal appellate courts direct judicial review],” he said.