In the wake of the U.S. Supreme Court's decision in Solid Waste Agency of Northern Cook County v. U.S. Army Corps of Engineers (SWANCC), courts have scrambled to reevaluate the scope and reach of the government's regulatory authority over "navigable waters" pursuant to the Clean Water Act (CWA). A growing majority of courts, especially the U.S. Court of Appeals for the Fourth Circuit, the U.S. Court of Appeals for the Sixth Circuit, the U.S. Court of Appeals for the Seventh Circuit, and the U.S. Court of Appeals for the Ninth Circuit, have read the decision narrowly, interpreting it as merely invalidating a controversial 1986 regulation allowing the U.S. Army Corps of Engineers (the Corps) to assert jurisdiction over isolated wetlands based on their use by migratory birds (the migratory bird rule). These courts hold that SWANCC's reasoning for invalidating the migratory bird rule as an invalid jurisdictional basis centered on the use of isolated waters by migratory birds. Therefore, they read the "significant nexus" language in SWANCC to mean any nexus to "waters of the United States" even if such nexus is based on an indirect hydrologic connection or some other U.S. Commerce Clause connection other than use by migratory birds.

A significant minority of courts, including the U.S. Court of Appeals for the Fifth Circuit, have instead read SWANCC broadly as restricting the authority of the Corps and the U.S. Environmental Protection Agency (EPA) over waters and wetlands that are a significant distance from traditionally navigable waters. These courts read SWANCC as "reining in" the historical expansion of federal jurisdiction since 1972 with the Corps' revisions of its regulations in 1975, 1977, and 1986. They hold that the Corps has expanded its jurisdiction to waters and wetlands a distance from traditionally navigable waters, misconstruing the congressional intent underlying the CWA. These courts generally conclude that while not all regulated waters must be navigable-in-fact, the government must show that a "significant nexus" exists between the waters sought to be regulated and a navigable waterway and that tenuous and indirect linkage is not sufficient to confer CWA jurisdiction.

While the courts have been grappling with SWANCC, the Bush Administration and the U.S. Congress have also "jumped into the fray." In January 2003, the Corps and EPA released a long-awaited guidance memorandum and an advance notice of proposed rulemaking (ANPRM). Congress has also recently begun considering legislation that would "fill the gap" created by the SWANCC decision.