A series of polyvinyl alcohol (PVA)/Fe3O4-coated cellulose acetate mixed matrix membranes were analyzed for Cd and Ni removal, both experimentally and theoretically. The effect of the coating layer on the metal ion rejection performance was investigated using molecular modeling approaches. Lower energy requirements for the detachment of ions from the coating layer were calculated. Our results imply that the coating layer interacts with metal ions to a much lower extent than the substrate layer does. Smaller mean square displacement data were calculated in the coating layer than in the substrate layer, which indicates a lower diffusivity of ions in the coating layer. This in turn shows the coating layer efficiently prevents ion transfer and provides higher retention/rejection. We conclude that applying a coating layer with lower Fe3O4 content would enhance the ion rejection performance of cellulose acetate mixed matrix membranes. The addition of Fe3O4 particles increases the number of active sites and the surface area, while a high content of these particles must be avoided as they may surround functional groups of polymer chains and also increase the porosity, which decreases the rejection performance of membranes.