In the separation of an anionic surfactant, ammonium perfluoroalkyl carboxylates from the residual aqueous solution in poly(tetrafluoroethylene) (PTFE) emulsion polymerization, reverse osmosis (RO) process was carried out by using three kinds of charged membranes, that is, anionic, cationic and nonionic membranes. Sodium alginate (SA), chitosan (CS) and poly(vinyl alcohol) (PVA) were prepared as the anionic, cationic and nonionic membranes, respectively. The permeation behaviors were investigated with the charge characteristics of the membranes in terms of electrostatic interaction between permeant and membrane, namely, Donnan potential. Also, the effects of operating condition, such as, feed pressure, feed concentration and permeation rate, have been discussed in terms of membrane fouling and concentration polarization.