For the last several years, federal circuit courts have debated the exact jurisdictional scope of §404 of the Clean Water Act (CWA), which authorizes the Secretary of the U.S. Army (the Army), acting through the U.S. Army Corps of Engineers (the Corps), to issue permits "for the discharge of dredged or fill material into the navigable waters at specified disposal sites." The circuit courts have based their debates on the assumption, well-supported by earlier CWA decisions, that Congress intended the term "navigable waters" within the CWA to extend to the limits of the U.S. Commerce Clause. This interpretation of "navigable waters" gives the agencies that administer the CWA much broader jurisdiction over water pollution than federal agencies have traditionally exercised through other statutes focused on "navigable waters," such as the Rivers and Harbors Act of 1899. It also rather immediately requires courts to assess CWA jurisdiction in terms of the ordinary constitutional Commerce Clause analysis.

The factual basis for the most recent debates on the Corps' CWA jurisdiction has been the Corps' assertion of jurisdiction over isolated wetlands through the so-called migratory bird rule. Pursuant to the migratory bird rule, the Corps claimed jurisdiction over isolated wetlands—that is, wetlands with no direct hydrological connection to other waters—if those wetlands served as habitat for birds protected by the Migratory Bird Treaty Act, birds that migrated across state lines, or endangered species. As such, the migratory bird rule clearly dispenses with any traditional "navigable waters" requirement that the subject waters be navigable in fact or subject to the ebb and flow of the tide.