Current and future court challenges to the “waters of the U.S.” rule must be heard in federal district courts, not circuit courts of appeals, the Supreme Court said Monday in a unanimous decision that ultimately could lead to lawsuits filed all over the country.

The court did not buy the arguments of the federal government, most environmental groups and some states that federal appeals courts are the proper venue for litigation over the rule, which has been blasted by the vast majority of farm groups as overly broad but supported by conservation groups that say it strikes the proper regulatory balance.

The decision sets up a battle in the 6th Circuit Court of Appeals over a nationwide stay of the WOTUS rule that the court issued in October 2015. Because the Supreme Court said that jurisdiction for WOTUS litigation lies in the district court, that means the 6th Circuit will almost certainly have to dissolve its stay when the Supreme Court decision is formally sent back to the appeals court.

“This Supreme Court decision brings greater clarity to an important issue that has bogged down the litigation over this and other Clean Water Act regulations for years,” said American Farm Bureau Federation counsel Ellen Steen in a news release. “That is a positive result, but it also creates uncertainty and confusion in the short term, because the 6th Circuit must soon lift its nationwide stay of the 2015 rule.”

Steen pointed out that EPA has yet to finalize two rules: one to delay the effective date of the WOTUS rule for two years, the other to rescind the rule entirely. The Supreme Court’s decision is likely to lead publication of one or both of those rules relatively soon.

EPA says there's no reason to be concerned.

“The Trump administration’s stay of the 2015 WOTUS rule will very likely be complete before any change in court jurisdiction can be finalized, or the Obama administration’s overreaching definition of WOTUS can be implemented,” EPA spokesperson Liz Bowman said in a statement.

And EPA Office of Water Administrator David Ross told Politico that he expected the “delay” rule would be finalized within a month.

There may nonetheless be a fight over the 6th Circuit’s stay of WOTUS. Even though many of those challenging the rule argued in favor of district court jurisdiction, they don’t want to see the nationwide injunction disappear, either.

Scott Yager, environmental counsel at the National Cattlemen’s Beef Association, said NCBA will be discussing its next move with litigation counsel, but that it may oppose dissolving the 6th Circuit’s stay.

However, former Justice Department attorney Stephen Samuels, who spent decades working on Clean Water Act issues, said the Supreme Court decision makes it “pretty clear that (the 6th Circuit) doesn’t have jurisdiction to issue a stay of the Clean Water Rule.”

Thirteen states that obtained an injunction from a federal district court in North Dakota halting WOTUS are likely to return to that court asking it to reinstate its injunction or expand it to apply nationwide, Samuels said. That court's injunction was no longer effective after the 6th Circuit assumed jurisdiction.

But the Justice Department has taken a high-profile position arguing that, in the case of President Donald Trump’s executive order targeting immigrants from certain countries, district courts cannot issue nationwide injunctions.

One of the government’s arguments for appellate court jurisdiction cited judicial efficiency.

“We acknowledge that routing WOTUS Rule challenges directly to the courts of appeals may improve judicial efficiency,” the Supreme Court said in its decision. “But efficiency was not Congress’ only consideration. Had Congress wanted to prioritize efficiency, it could have authorized direct circuit-court review of all nationally applicable regulations, as it did under the Clean Air Act.”

Ultimately, however, the court ruled that the language of the Clean Water Act clearly does not allow suits challenging rules such as WOTUS to be brought in the appeals courts.

The law lists seven actions that are reviewable in the courts of appeals, including the approval or promulgation of “any effluent limitation or other limitation” under four sections of the law, and the issuance or denial of “any permit under Section 1342 of this title," which deals with National Pollutant Discharge Elimination System (NPDES) permits, not wetlands permits.

“Congress made clear that rules like the WOTUS Rule must be reviewed first in federal district courts,” the high court said.

Once all the legal wrangling over jurisdiction dies down and a new Clean Water Rule is in place, the legal landscape could be filled with competing litigation in different district courts.

Then the fate of wetlands regulation will likely play out in district courts around the country, “and that will take time,” Samuels said.