Ion exchange membranes were fabricated using a phase inversion technique based on polyvinyl chloride nanocomposites. Subsequently, electrodialysis membranes were modified by the addition of [SiO2-co-Ag] nanoparticles using magnetron sputtering. The impact of varying concentrations of [SiO2-co-Ag] nanoparticles on the performance of mixed-matrix poly (vinyl chloride)-based nanoparticle cation exchange membranes was studied. Various techniques, including scanning electron microscopy (SEM), atomic force microscopy (AFM), and scanning optical microscopy (SOM) confirmed the presence of nanoparticles in the structure of membranes. The SEM images showed that the addition of SiO2-co-Ag nanoparticles resulted in a more compact structure for the modified membranes. The SOM images show that the fabricated membranes had a uniform surface and uniform distribution of SiO2-Ag in the membrane matrix. The AFM images revealed that the modified membranes had a rough surface at high additive concentrations (4.0% wt.) and cross-sectional SEM images confirmed that the addition of nanoparticles created cracks and cavities in the membrane structure. The hydrophilicity of silica and silver nanoparticles increased the surface hydrophilicity of the modified membranes. The membrane potential, permselectivity, and transport number showed fluctuations, decreasing initially with the use of SiO2-co-Ag nanoparticles up to a concentration of 1.0% wt and then increasing with an increase in the concentration of nanoparticles to 2.0% wt before declining again for a concentration of 4.0% wt. The flux and ionic permeability were promoted by the addition of SiO2-co-Ag up to 1.0% wt, but after that, they showed a decreasing trend with an increase in the concentration of nanoparticles. The areal electrical resistance of the prepared membrane dramatically declined with an increase in the concentration of SiO2-Ag. Importantly, the application of these membranes was in electrodialysis, and the use of also enhanced the mechanical resistance of the membranes. Furthermore, the fabricated membranes exhibited a good ability to remove E. coli from water. Notably, the modified membrane with a 1.0% wt concentration of SiO2-co-Ag nanoparticles demonstrated greater performance in removing E. coli. [ABSTRACT FROM AUTHOR]