Collectively, the millions of wetlands in the prairie pothole region create one of the most important waterfowl breeding areas in North America. Their use by migratory waterfowl provided a legal rationale, the Migratory Bird Rule, for extending Clean Water Act Section 404 protection to them even though prairie potholes are generally not associated with navigable waters. The U. S. Supreme Court's decision in the case of the Solid Waste Agency of Northern Cook County vs. U. S. Army Corps of Engineers, the SWANCC decision, seems to have invalidated the use of the Migratory Bird Rule. We have evaluated the adjacency of potholes to navigable waters and the implications of the SWANCC decision. For most groups of wetland organisms, with the important exception of fish, potholes are not ecologically isolated habitats. Their flora and fauna and functions (primary production, food webs, mineral cycling, water storage capacity, etc.) are largely determined by water levels, not degree of isolation. Annual changes in precipitation can significantly change their water levels, and this can result in major shifts in their flora and fauna. Hydrologically, prairie potholes are usually connected by ground-water flows and, during wet years, even by surface-water flows. According to landscape analyses done by Ducks Unlimited on selected areas in North and South Dakota, most prairie potholes are not adjacent to (>95%) or even within 1 km (ca. 50%) of navigable waters. Consequently, because of SWANCC, most prairie potholes may no longer be protected under section 404 of the Clean Water Act. Most prairie potholes, however, are located on farms and are thus protected by the Swampbuster provision of the 1985 Food Security Act. Even with Swampbuster, there will be minor losses of potholes without any mitigation around cities and towns, and various exemptions under Swampbuster will result in some loss or degradation of prairie potholes. The SWANCC decision, however, will significantly weaken the protection of prairie potholes because it lends strength to existing pressures to weaken or eliminate Swampbuster.