Cation exchange polymeric matrices are widely used in water treatment protocols to reduce the mineral content of hard waters, even for human consumption. However, they are not antibacterial and flowing bacteria can be trapped in their structures and proliferate, thus acting as microbial contamination sources. Here, Ag@Co-nanoparticles (Ag@Co-NPs) with a low-cost superparamagnetic Co0-core and an antibacterial Ag-shell are synthesized on granulated cation exchange polymeric matrices under soft reaction conditions. The presence of these NPs provides the final nanocomposite (NC) with additional functionalities (superparamagnetism and antibacterial activity) making it ideal for water purification applications. Ag@Co-NPs are synthesized in situ on four cation exchange polymeric matrices containing either strong (sulfonic) or weak (carboxylic) acid functional groups homogeneously distributed (C-type) or concentrated on an external shell (SST-type) by the intermatrix synthesis (IMS) method. The NCs are characterized (metal content, NP size and distribution, metal oxidative state, and metal release) and evaluated for water purification applications.