This past January, the U.S. Supreme Court held that the Clean Water Act (CWA) did not authorize the federal government to prohibit a landfill operator from filling isolated ponds on its property merely because the ponds were used as habitat by migratory birds. The National Association of Home Builders claimed that the decision in Solid Waste Agency of Northern Cook County v. U.S. Army Corps of Engineers (SWANCC) was "a major legal victory for home builders and other private property owners." Critics of the SWANCC decision argued that it jeopardizes "perhaps a fifth of the water bodies in the United States." The timing of the Court's decision was particularly disheartening to wetlands protection advocates, since the ruling was announced shortly after the U.S. Fish and Wildlife Service (FWS) released a report that indicated that the annual rate of wetlands loss has been declining steadily.

While the ruling will primarily impact federal wetlands regulation, the Court's holding applies to isolated waters, in general, and not merely to isolated wetlands. Further, while the SWANCC case merely examined the federal government's authority to prohibit the filling of isolated waters under §404 of the CWA, the reasoning of the Court precludes the federal government from regulating any pollution of isolated waters that are within the reach of the ruling. The Court concluded that the U.S. Army Corps of Engineers (the Corps) could not prohibit the filling of the ponds because they were not "navigable waters," as defined in the statute. Since the term "navigable waters" is used throughout the statute, the Court's ruling has implications for the §402 national pollutant discharge elimination system (NPDES) permit program, and for the rest of the statute.