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Abstract Perfluoroalkyl and polyfluoroalkyl substances (PFASs) are now widely found in aquatic ecosystems, including sources of drinking water and portable water, due to their increasing prevalence. Among different PFAS treatment or separation technologies, nanofiltration (NF) and reverse osmosis (RO) both yield high rejection efficiencies (>95%) of diverse PFAS in water; however, both technologies are affected by many intrinsic and extrinsic factors. This study evaluated the rejection of PFAS of different carbon chain length (e.g., PFOA and PFBA) by two commercial RO and NF membranes under different operational conditions (e.g., applied pressure and initial PFAS concentration) and feed solution matrixes, such as pH (4–10), salinity (0‐ to 1000‐mM NaCl), and organic matters (0–10 mM). We further performed principal component analysis (PCA) to demonstrate the interrelationships of molecular weight (213–499 g·mol⁻¹), membrane characteristics (RO or NF), feed water matrices, and operational conditions on PFAS rejection. Our results confirmed that size exclusion is a primary mechanism of PFAS rejection by RO and NF, as well as the fact that electrostatic interactions are important when PFAS molecules have sizes less than the NF membrane pores. Practitioner PointsTwo commercial RO and NF membranes were both evaluated to remove 10 different PFAS.High transmembrane pressures facilitated permeate recovery and PFAS rejection by RO.Electrostatic repulsion and pore size exclusion are dominant rejection mechanisms for PFAS removal.pH, ionic strength, and organic matters affected PFAS rejection.Mechanisms of PFAS rejection with RO/NF membranes were explained by PCA analysis.