For over two decades, courts and agencies have assumed that the Clean Water Act (CWA) grants the U.S. Environmental Protection Agency (EPA) and the U.S. Army Corps of Engineers (Corps) jurisdiction over the nation's waters to the full extent of the U.S. Congress' authority under the U.S. Constitution's Commerce Clause. This belief led the Corps and EPA to assert CWA jurisdiction over virtually all waters in the nation, including navigable waters; non-navigable tributaries; adjacent wetlands; and non-navigable, isolated, intrastate waters and wetlands.

In early 2001, however, the U.S. Supreme Court rejected the Corps' assertion of authority over a non-navigable, isolated, intrastate water in Solid Waste Agency of Northern Cook County v. U.S. Army Corps of Engineers (SWANCC). The Corps had claimed jurisdiction under its "migratory bird rule," which asserted jurisdiction over waters that, among other things, "are or would be used as habitat by . . . migratory birds which cross state lines." Pointing to statements in the Act's legislative history that the term "navigable waters" was to be given "the broadest possible constitutional interpretation, unencumbered by agency determinations which have been made or may be made for administrative purposes," the Corps defended the migratory bird rule as an exercise of federal power over things having a "substantial effect" on commerce—the broadest basis of federal power under the Commerce Clause. Rejecting this argument, the Supreme Court held that Congress did not intend to exercise its power over things "affecting commerce" in passing the CWA. Instead, according to the Court, Congress intended to exercise only its authority over navigation.