Wassataquoik Stream flows through Township 3, Range 8, Maine, on land owned by environmentalist Roxanne Quimby, founder of Burt’ss Bees. (Robert F. Bukaty/Associated Press)

The Obama administration again signaled Friday that it was going out fighting for its environmental legacy, filing a 245-page brief in defense of its controversial “Waters of the United States” rule that defines every water body in the nation, and determines whether they can be regulated under the Clean Water Act.

The rule, jointly issued by the Environmental Protection Agency and the Army Corps of Engineers in 2015, was immediately challenged in federal court by North Dakota, Wyoming, Alaska and other states, resulting in a nationwide stay issued last year by a federal appeals court in Ohio.

Friday’s brief filed by Department of Justice Assistant Attorney General John Cruden is the administration’s most forceful defense of the rule. But how it will be defended in the Sixth Circuit Court of Appeals was not clear, because both President-elect Donald Trump and his nominee to lead the EPA, Scott Pruitt, oppose the rule.

Cruden said that by filing the brief, the court now has to consider it, and the lawyers prosecuting the case for the current administration will still be around to do so. To undo a rule, Cruden said, the Trump administration would have to take the same arduous path that the EPA and Army Corps took to create it.

They analyzed 1,200 peer-reviewed studies, deciding which waters constituted navigable waters, interstate waters or territorial seas. They determined which waters comprised lakes, ponds, wetlands or small waters that could only be defined on a case-by-case basis. Hundreds of hearings were held and at least a million comments were submitted in the run-up to the final rule.

Advocates of farmers said the rule was highly confusing because it defined areas as water bodies even when water was not present, and had not been for years. Farmers would not know whether their practices were being regulated or not.

State attorneys general were livid. North Dakota’s attorney general derisively claimed that even prairie potholes could fit the description of a water body. He called it a federal “power grab” that would not lead to cleaner water in his state.

WOTUS, as the rule is known, stems from a 2006 Supreme Court case involving a Michigan developer who fought an EPA fine for filling 54 acres of wetlands without a permit to build a shopping center. The EPA and the Army Corps argued that the wetlands were covered by the 1972 Clean Water Act, but the court said the law’s reach was unclear.

In an opinion, two justices wrote that all bodies of water “with a significant nexus” to “navigable waters” are covered by the act. The new rule was drafted to end confusion over the meaning of “significant nexus.”

Creating WOTUS, the Justice Department brief argues, was an attempt to make a rule that is “clear and understandable and protects the nation’s waters, supported by science and consistent with the law.” In other words, it sought to clear up confusion identified by the justices.

The legal challenge by nearly two dozen states, and another challenge by conservation groups that said the rule doesn’t do enough to protect endangered animals, “should be denied because the rule is not arbitrary, capricious, or otherwise contrary to law,” the brief argues.

But it hedged a little, in case the judges saw merit in some areas and not others. If some of the challenges have merit in the court’s eyes, the brief goes on to say, “the court should not automatically vacate the entire rule,” as some opponents contend.