There is increasing concern about occurrences of perfluorinated compounds (PFCs) in the environment due to their persistent, bioaccumulation, and potentially toxic effects. We investigated contamination of 11 PFCs (C4-C12) in the Yodo River system, which is a major source of drinking water for more than 11 million people of Kansai region in Japan. PFCs were detected in higher concentration even exceeding more than 1000 ng/L in some cases. Composition profile of total PFCs concentration showed that PFOS, PFHxA, PFOA, and PFNA were occurring dominantly in the river system. PFOS and PFOA concentration were nearly proportional to a previous study in the same river system, indicating continuous sink of the compounds into the river system. Although discharge of PFCs from wastewater effluents at upstream could be one of the major point sources, concentration did not exceed 29.4 ng/L at the downstream of main Yodo River, possibly, due to dilution effects. Total mass load of PFCs in mainstream of Yodo River was estimated 451.7 g/d based on observed river discharge and PFCs concentration. Results showed that Yodo River system could have a unique upstream-downstream linkage of PFCs contamination and the river could be a continuous pathway of PFCs exposure to the people of Kansai region.