The Solid Waste Agency of Northern Cook County (SWANCC) (plaintiff), a consortium of 23 suburban Chicago cities and municipalities, purchased a 553-acre parcel of property (the site) for the purposes of developing a fill disposal site for baled nonhazardous solid waste. The site, formerly a sand and gravel mining pit, contained permanent and seasonal ponds of varying sizes. SWANCC contacted the U.S. Army Corps of Engineers (Corps) (defendant) to determine whether a fill permit was required under § 404(a) of the Clean Water Act (CWA). Initially, the Corps determined that it lacked jurisdiction to issue a permit because the ponds were not “navigable waters” as defined in the CWA. However, after learning that the site contained several species of migratory birds, the Corps reconsidered their position and asserted jurisdiction under § 404(a) which extended to waters used as a habitat for migratory birds that cross state lines, known as the Migratory Bird Rule. The Corps refused to issue a permit to SWANCC. SWANCC filed suit in federal court under the Administrative Procedure Act challenging the Corps’ assertion of jurisdiction over the site and the merits of the permit denial. The district court granted summary judgment in favor of the Corps. SWANCC appealed. The court of appeals affirmed. The U.S. Supreme Court granted certiorari to review.