A three-judge panel of the Sixth Circuit has decided that jurisdiction over the legal challenges to the “Waters of the U.S.” rule lies in that court — not in the district courts as industry groups and most state governments have argued. The court’s decision came in the form of three separate opinions, one by each of the three judges involved, and each with a different view of the law on this complex issue. Given the diversity of opinions among these three judges, and given the importance of the issues at stake, it seems highly likely that one or more parties will file a petition for rehearing by the full Sixth Circuit. Meanwhile, the temporary stay of the WOTUS rule previously issued by the Sixth Circuit presumably will remain in effect.  
It seems almost certain that state governments or industry groups — or both — will seek rehearing by the full Sixth Circuit, and it seems likely that the issue could go on to the U.S. Supreme Court. However the jurisdictional question is finally resolved, the parties — especially the plaintiffs—have a strong interest in achieving certainty that they are in the correct court before proceeding with the time-consuming and costly process of litigating the merits of the WOTUS rule.
Any petition for rehearing must be filed within 45 days. If the Sixth Circuit or the Supreme Court ultimately rule that the appellate court does not have jurisdiction, the various legal challenges will proceed in the federal district courts, the nationwide stay of the rule will end, and many of the plaintiffs presumably will ask those district courts for temporary relief from the WOTUS rule.