Perfluoroalkyl acids (PFAAs) are widely detected in the environment, especially in estuarine and coastal areas where fluctuation of salinity occurs. Salinity alteration affected the distribution of PFAAs and even the bioaccumulation in organisms. However, the inner mechanism is still unclear. In this study, the marine medaka (Oryzias melastigma), a euryhaline fish model, was exposed to four PFAAs congeners under three different salinities (0, 15 and 35？psu). Results showed that the bioaccumulation of PFAAs increased in fish as the water salinity increased. PFAAs with longer lengths of carbon？fluorine bond showed higher bioaccumulation in the fish. Salinity did not alter the levels of PFAAs in water media, however, the uptake rate of PFAAs from gills did increase with the salinity. Further analysis of the mechanism showed that PFAA bound to branchial proteins as confirmed by fluorescence spectroscopy. Higher expressions of proteins binding to PFAAs including organic anion transporter 1 (OAT1) and fatty acid-binding protein (FABP) facilitated the uptake of PFAAs through gills in fish culturing under higher salinity. In all, our study showed that elevation of salinity can induce the expression of proteins binding to PFAAs in gills, thus facilitate the uptake of water PFAAs. Salinity fluctuation should be taken into consideration when assessing the chemical risk in the estuarine and coastal areas.