In this research, mixed matrix cation exchange membranes were prepared by the solution casting technique using polyvinylchloride (PVC) as base binder, resin powder as functional groups agent, iron-nickel oxide nanoparticles as adsorptive filler and silver (Ag) nanolayers as surface modifier. Ag nanolayer was deposited on the membrane surface by the magnetron sputtering method. The effects of nanolayer deposition rate (low, medium and high) on physicochemical and antibacterial characteristics of the membranes were studied. X-ray diffraction (XRD) results revealed that membrane crystallinity was improved with increase in deposition rate. In addition, atomic force microscopy (AFM) results showed that membrane roughness was decreased by increase in deposition rate. Membrane selectivity was slightly enhanced by increase in Ag nanolayer deposition rate in modified membranes. Ionic fluxes were also increased by increase in Ag nanolayer deposition rate in membranes. Moreover, membranes containing Ag nanolayers showed good ability in Escherichia coli removal. The Ag nanolayer-modified membranes at a high deposition rate showed better performance compared to others.