Nanofiltration was thought to be a good option for the recovery of perfluorohexanoic acid (PFHxA) from industrial wastewater. In this study, two commercially available nanofiltration (NF) membranes (NF 270 and NTR-7450) were tested to concentrate the PFHxA in aqueous solution. Filtration test was conducted in crossflow filtration mode. Membrane flux and PFHxA rejection rate were monitored throughout the filtration test. The impact of initial feed water pH on membrane performance was investigated. Results demonstrated that the two NF membranes showed different response to the change of initial feed water pH, which was caused by the intrinsic properties of membrane material. The flux performance of NF 270 was stable, while its rejection rate of PFHxA was very sensitive to the change of initial feed water pH. Opposite result was obtained with NTR-7450. It had a very good stability on rejection rate, while its flux was very sensitive to the change of initial feed water pH. The mechanisms behind these phenomena were also discussed. The results obtained in this study should be very useful for the process design in practical engineering.