The federal Clean Water Act (Act) prohibited the discharge of pollutants into protected waters, unless the discharger first obtained: (1) state certification and (2) a permit from the United States Environmental Protection Agency (EPA) (defendant). For purposes of the Act, Puerto Rico was a state. Puerto Rico Sun Oil Company (Sun) (plaintiff) sought Puerto Rico's certification and an EPA permit for Sun's discharges. State governments and the EPA usually allowed dischargers to measure their discharges in a mixed zone. Mixed-zone measurement was of vital importance to Sun. After an unusually long and mistake-ridden process, Puerto Rico certified Sun's application. However, Puerto Rico’s certificate omitted any mixed-zone provision. It was unclear if the omission was deliberate, a mistake, or maybe related to an ongoing review that Puerto Rico was conducting into its mixed-zone policy. At Sun's request, Puerto Rico agreed to complete the policy review and then consider revising Sun's certification to permit mixed-zone measurement. Puerto Rico provided the details of this agreement to the EPA. Although Puerto Rico eventually decided to revise Sun's certification and allow mixed-zone measurement, the EPA issued a permit to Sun before Puerto Rico made that decision. The EPA permit omitted a mixed-zone provision. Sun asked the EPA to review that omission. After review, the EPA still refused to revise Sun's permit. Sun then appealed to the United States Court of Appeals for the First Circuit.