The influence of salinity and organic matter on the distribution coefficient (Kd) for perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) in a brackish water–clay system was studied. The distribution coefficients (Kd) for PFAs onto inorganic clay surfaces increased with salinity, providing evidence for electrostatic interaction for the sorption of PFAs, whereas the relationship between Kd and organic carbon content (foc) suggested that hydrophobic interaction is the primary driving force for the sorption of PFAs onto organic matter. The organic carbon normalized adsorption coefficient (Koc) of PFAs can be slightly overestimated due to the electrostatic interaction within uncoated inorganic surfaces. In addition, the dissolved organic matter released from coated clay particles seemed to solvate PFA molecules in solution, which contributed to a decrease in Kd. A positive relationship between Kd and salinity was apparent, but an empirical relationship for the ‘salting-out’ effect was not evident. The Kd values of PFAs are relatively small compared with those reported for persistent organic pollutants. Thus, sorption may not be a significant route of mass transfer of PFAs from water columns in estuarine environments. However, enhancement of sorption of PFAs to particulate matter at high salinity values could evoke potential risks to benthic organisms in estuarine areas.