The study concerned surface water contamination of two perfluorinated compounds: perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA). Surveys were repeatedly conducted in the Yodo River basin in order to find out the contamination profiles and the sources of these compounds. Collected samples were analyzed for aqueous PFOS and PFOA concentrations, by solid phase extraction (SPE) coupled with LC/MS measurement, and other fundamental water quality parameters. PFOS and PFOA concentrations were measured from 0.4 to 123 ng/L and from 4.2 to 2600 ng/L, respectively. The concentrations were reproducible and the highest levels were found in effluents of some sewage treatment plants (STPs) and tributary streams. PFOA concentration was often higher than that of PFOS, but their profiles in the basin were somewhat similar. Both profiles were different from those of chloride, and DOC suggesting that there could be little relation between contamination of PFOS and PFOA in the basin with population and nature. Loads estimation revealed that main sources of the contaminants in Katsura River were three STP effluents while the sources in Uji River could be from Lake Biwa. It is suggested that other wastewaters than domestic wastewater contributed significant loads of PFOS and PFOA in highly contaminated STP effluents.