President Obama’s push to extend the EPA’s regulatory hand to ditches and small streams to enforce clean water rules was blocked Thursday by a federal judge, who said the administration had overstepped its bounds in trying yet another end run around Congress.

Judge Ralph R. Erickson called the Environmental Protection Agency’s attempt “inexplicable, arbitrary and devoid of a reasoned process,” and issued an injunction preventing the EPA and the U.S. Army Corps of Engineers from claiming oversight of millions of acres of land that contain small bodies of water.

The EPA, though, said it will only honor the injunction in the 13 states that had sued, and will move forward with the rules in the rest of the country.

“In all other respects, the rule is effective on August 28,” the agency said in a statement. “The agencies are evaluating these orders and considering next steps in the litigation.”

Known as the Waters of the United States — or what critics call WOTUS for short — the new rules have been controversial from the start.

The Obama administration said it was trying to clear up confusion after an earlier court decision left it unclear how far the federal Clean Water Act stretched. That law gives the EPA power over “navigable” waters and any land where water runs off into those waters. But what that meant has been hotly debated.

Last year the administration wrote new definitions that would have subjected all waters within 4,000 feet of a navigable water to EPA review and control.

Critics said that would mean the EPA would control lands near ditches with no possible connection to the rivers and lakes that the law was designed to protect. The states that sued said the new rules would create a nightmare scenario of having to get permits and perform environmental studies on every gas or water pipeline, or reclamation or development project.

Judge Erickson, who sits in federal district court in North Dakota, said he’d looked at all the evidence he could, and couldn’t see how the EPA justified the 4,000-foot standard.

“The rule asserts jurisdiction over waters that are remote and intermittent waters. No evidence actually points to how these intermittent and remote wetlands have any nexus to a navigable-in-fact water,” he wrote.

He said the change in definition was big enough that the administration should have gone through a full public notice and comment period.

Judge Erickson is the latest in a long list of federal judges to rule Mr. Obama overstepped his boundaries in pursuing his domestic agenda.

A federal court in Texas has halted the president’s November 2014 deportation amnesty, also finding, like Judge Erickson, that the immigration changes should have gone through public notice and comment.

Federal courts are also still hearing cases challenging the legality of how Mr. Obama is carrying out Obamacare and the way his State Department handled former Secretary Hillary Rodham Clinton’s emails.

Republicans on Capitol Hill, who have long opposed the president’s plans to expand the reach of the EPA, cheered the judge’s ruling.

“The Waters of the United States rule is unlawful and an abuse of executive power,” said Julia Slingsby, spokeswoman for the House Natural Resources Committee. “The judge’s decision to block the rule — which was challenged by 13 states — is encouraging, especially as EPA’s credibility has been questioned in the past month. The EPA needs to be stopped before it does more harm to our nation’s precious water resources.”

The EPA is still dealing with an embarrassing spill from the Gold King Mine, which was an agency project to recover the abandoned mine. Pressure built up behind a pile of debris, spewing millions of gallons of toxic water into the Animas River and downstream bodies of water.

EPA officials say they’re holding themselves to a high standard in trying to correct the damage from the mine spill.

And agency officials defend the water rules as important protections, saying that nearly one-third of Americans get their drinking water from streams that were “vulnerable to pollution” before their proposal.

“We need clean water upstream to have healthy communities downstream. The health of rivers, lakes, bays, and coastal waters depend on the streams and wetlands where they begin,” the agency said.

In order to issue his injunction, Judge Erickson first had to find that he could hear the case in district court. The administration argued it should have gone straight to an appeals court instead.

Two other federal district courts have sided with the administration on the jurisdiction question, the EPA said.

The 13 states that were part of the suit, and where the EPA says it won’t follow through on the new rules, are: Alaska, Arizona, Arkansas, Colorado, Idaho, Missouri, Montana, Nebraska, Nevada, New Mexico, North Dakota, South Dakota and Wyoming.

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