Does the use by migratory birds of isolated, intrastate waters establish enough of a connection to "navigable waters" and interstate commerce to permit federal regulation under the Clean Water Act (CWA) and the U.S. Commerce Clause? The U.S. Army Corps of Engineers thinks so, but courts and commentators have not been entirely sympathetic to the Corps' so-called migratory bird rule. The Fourth Circuit and U.S. Supreme Court Justice Thomas (in a dissent from denial of certiorari) have rejected such a broad jurisdictional reach in no uncertain terms. Even the Ninth Circuit, one of two federal courts of appeal to approve the migratory bird rule, has recognized that it "certainly tests the limits of Congress's commerce powers and, some would argue, the bounds of reason." And many academic commentators question whether the rule is constitutional after United States v. Lopez, which arguably ushered in an era of more demanding review of federal action under the Commerce Clause.

On May 22, 2000, the Supreme Court agreed to hear a challenge to the rule presented in Solid Waste Agency of Northern Cook County v. United States Army Corps of Engineers (SWANCC). In that case, the U.S. Court of Appeals for the Seventh Circuit held that the CWA gives the Corps jurisdiction over isolated waters that are neither navigable nor connected or adjacent to navigable waters, but that provide habitat for birds that cross state lines or are protected by Migratory Bird Treaties. The Seventh Circuit also held that this vast extension of the Corps' jurisdiction does not exceed the federal commerce power.