Two nanofiltration (NF90 and Nano-Pro-3012) membranes were investigated for their capacity to removemetal ions. This study presents the effect of membrane roughness on the removal of toxic metal ions during dead endmembrane filtration. Atomic force microscopy, scanning electron microscopy, WSXM software and ImageJ were usedto characterize the roughness of the membranes. Gradual decrease in filtration permeate flux was observed as foulantsaccumulated at the interface of the membranes; filtration permeate flux varied from 20 L/m2/h to 14 L/m2/h and 11 L/m2/h to 6 L/m2/h for NF90 and Nano-Pro-3012, respectively. NF90 membrane was more prone to fouling than the Nano-Pro-3012 membrane: the percentage flux reduction was higher for NF90 (3.6%) than Nano-Pro-3012 (0.98%). Thebearing ratio of the fouled NF90 exhibited a high peak of 7.09 nm than the fouled Nano-Pro-3012 with the peak of6.8 nm.