Perfluorinated compounds (PFCs), such as perfluorooctane sulfonate (PFOS), perfluorooctanoate (PFOA), perfluorononanoate (PFNA), perfluorohexane sulfonate (PFHS), and perfluorooctane sulfonamide (PFOSA) are widely distributed in aquatic ecosystems. Despite studies reporting the occurrence of PFCs in aquatic organisms, the fate of PFCs in tidal flat and marine coastal ecosystems is not known. In this study, we determined concentrations of PFOS, PFOA, PFNA, PFHS, and PFOSA in sediments; benthic organisms, including lugworm, mussel, crab, clam, oyster, and mudskipper fish from tidal flat; and shallow water species, such as filefish, bream, flounder, shark, finless porpoise, gull, and mallard collected from the Ariake Sea, Japan. PFOS and PFOA were detected in most of the samples analyzed, followed by PFNA, PFOSA, and PFHS. In shallow water species, PFOS was the dominant contaminant, and elevated concentrations were found in higher trophic level species, such as marine mammals and omnivorous birds. These results suggest biomagnification of PFOS through the coastal food chain. In contrast, PFOA was the most abundant compound in tidal flat organisms and sediments. PFOA concentrations in sediments, lugworms, and omnivorous mudskippers in tidal flat were approximately 1 order of magnitude greater than the levels of PFOS. This indicates differences in exposure pattern and bioavailability of PFOS and PFOA between shallow water and tidal flat organisms. The accumulation profiles of PFCs were compared with those of organochlorines (polychlorinated biphenyls, PCB), organotin (tributyltin,TBT), and polycyclic aromatic hydrocarbons (PAHs) in tidal flat and shallow water samples collected from the Ariake Sea. Concentrations of PFCs in sediments and in tidal flat organisms were significantly lower than that found for PCBs, TBT, and PAHs. Nevertheless, PFOS concentrations in shallow water species were comparable to and/or significantly greater than those of other classes of contaminants. This implies that the aqueous phase is a major sink for PFCs, which is different from what was observed for nonpolar organic pollutants.