To evaluate the significance of reverse osmosis (RO) and nanofiltration (NF) surface morphology on membrane performance, productivity experiments were conducted using flat-sheet membranes and three different nanoparticles, which included SiO2, TiO2 and CeO2. In this study, the productivity rate was markedly influenced by membrane surface morphology. Atomic force microscopy (AFM) analysis of membrane surfaces revealed that the higher productivity decline rates associated with polyamide RO membranes as compared to that of a cellulose acetate NF membrane was due to the inherent ridge-and-valley morphology of the active layer. The unique polyamide active layer morphology was directly related to the surface roughness, and was found to contribute to particle accumulation in the valleys causing a higher flux decline than in smoother membranes. Extended RO productivity experiments using laboratory grade water and diluted pretreated seawater were conducted to compare the effect that different nanoparticles had on membrane active layers. Membrane flux decline was not affected by particle type when the feed water was laboratory grade water. On the other hand, membrane productivity was affected by particle type when pretreated diluted seawater served as feed water. It was found that CeO2 addition resulted in the least observable flux decline, followed by SiO2 and TiO2. A productivity simulation was conducted by fitting the monitored flux data into a cake growth rate model, where the model was modified using a finite difference method to incorporate surface thickness variation into the analysis. The ratio of cake growth term (k1) and particle back diffusion term (k2) was compared in between different RO and NF membranes. Results indicated that k2 was less significant for surfaces that exhibited a higher roughness. It was concluded that the valley areas of thin-film membrane surfaces have the ability to capture particles, limiting particle back diffusion.