Perfluoroalkyl acids (PFAs) are a family of highly persistent compounds which are present in the environment as a result of degradation of polyfluorinated precursors, from use as processing aids for production of fluoropolymers, and use in fire fighting foams. The purpose of this study was to investigate prevailing concentrations and possible sources of PFAs in Lake Superior, as well as in Siskiwit Lake on Isle Royale. Between 2001 and 2005, replicate water samples were taken from lake surface waters, and from depth profiles, as well as from major tributaries including municipal waste water treatment plants (WWTPs) at three major population centers. Perfluorooctanoate (PFOA) was the predominant PFA in Lake Superior, with concentrations ranging from 0.07 to 1.2 ng/L in surface waters. PFOA concentrations were generally 1.5 to 2-fold greater than perfluorooctanesulfonate (PFOS) levels. WWTPs were found to contribute up to 20 fold higher concentrations of PFOA (22 ng/L) relative to the intake water from Lake Superior, while most tributaries contained lower concentrations of perfluorocarboxylates (PFCA) and perfluoroalkylsulfonates (PFSs) (<0.1 ng/L). Overall tributaries and precipitation were estimated to be the major sources of PFCAs and PFSs to Lake Superior. Tributaries were estimated to be the largest source contributing 59% of PFOA and 57% of PFOS inputs to the lake. Profiles conducted over the deepest points in the lake showed that PFAs were found throughout the water column, however, there was no distinctive trend with depth.