Hindered (effective) diffusion of perchlorate anion (ClO4-) through negatively-charged porous nanofiltration and ultrafiltration membranes was determined by means of diffusion cell experiments. Three electrolytes, KCl, K2SO4, and CaCl2, were employed to determine their effects on the effective diffusion of perchlorate through membrane pores under varying pH levels (4, 6, 8, and 10). In addition, the effect of electrolyte concentration on effective diffusion was investigated, given that conductivity can affect electrostatic repulsion associated with the membrane surface/pore charge. All diffusion cell measurements were performed by reusing the same membrane in order to minimize artifacts from membrane variation based on membrane pore geometry (size) and membrane surface charge. In general, the results indicate that target ion (in this case ClO4-) transport by diffusion through the negatively charged membrane pores can be significantly affected by the presence of co- and counter ions and pH conditions, which significantly influence partitioning of the perchlorate ion due to mainly electrostatic repulsion occurring between the perchlorate anion and the negatively charged membrane.