Overruling Chevron doesn't require Congress to make laws covering every nuance. It just changes who resolves ambiguities in the laws. The irony of your comment is that federal clean-water legislation dates to 1948. The governing precedent at the time was Skidmore v. Swift, under which courts deferred to agency interpretations of statutes tot he extent the court found them persuasive. That regime functioned just fine for 40 years before Chevron changed the law.

Chevron, of course, was a case where the Reagan EPA interpreted the word "source" in the Clean Air Act to refer to an entire plant, rather than a distinct pollution source. The D.C. Circuit, in a decision written by Ruth Bader Ginsberg, disagreed with the EPA's interpretation of the law. The Supreme Court reversed, holding that the EPA was empowered to resolve such ambiguities in the text of the statutes.