Nanofiltration (NF) is a promising technology to remove the perfluoroalkyl acids, perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS) from water; however, little information is available as to how the natural water matrices impact PFOA and PFOS rejection when using NF. This study investigated the removal of PFOA and PFOS in laboratory-prepared water, surface water, and groundwater via NF to determine the effect of water matrix properties on PFOA and PFOS rejection by NF. PFOA and PFOS rejections were up to approximately 38% higher in the natural water matrices when compared to the laboratory-prepared water. The rejection of PFOA did not vary in the tested river water and groundwater; however, an increasing trend in PFOS rejection was observed and attributed to enhanced size exclusion of PFOS-cation complexes via the sulfonate (–SO3−) ‘head’ of the PFOS ions and cation-induced membrane fouling by natural organic matter. Compound rejection increased with declining flux that was consistent with the dissolved organic matter (DOM) content of the respective water matrices. This study confirmed that DOM and cations indigenous to natural water matrices can lead to improved rejection of PFOA and PFOS when using NF.