Despite ongoing efforts to develop robust analytical methods for the determination of perfluorinated compounds (PFCs) such as perfluorooctanesulfonate (PFOS) and perfluorooctanoic acid (PFOA) in surface water, comparatively little has been published on method performance, and the environmental distribution of these materials remains poorly described worldwide. In this study, an existing method was improved and applied in a large-scale evaluation of the Upper Mississippi River Basin, one of the largest watersheds in the world. Samples were collected in 2008 in an effort that involved multiple sample sites and collection teams, long-range transport, and storage of up to 4 weeks before analysis. Ninety-four percent of the resulting 177 samples had quantifiable PFC concentrations, with 80% of the individual target compounds below 10 ng/L. The most abundant PFCs were perfluorobutanoic acid (C4; 77% above the limit of quantitation, LOQ), perfluorooctanoic acid (C8; 73%), perfluorooctanesulfonate (PFOS; 71%), perfluorohexanoic acid (C6; 70%), and perfluoroheptanoic acid (C7; 69%), with the remaining target compounds occurring above the LOQ in less than 50% of the samples. The highest concentrations recorded include C4 at 458 ng/L, PFOS at 245 ng/L, and C8 at 125 ng/L, suggesting various point source inputs within the Basin.