This research focuses on the formation of ionic clusters and the transport properties of metal ions through electrodialysis heterogeneous cation exchange membrane modified by l-cysteine as a polar additive. The molecular electrostatic potential of l-Cyst and resin particle showed appropriate reactive sites for electrophilic and nucleophilic attacks. Furthermore, the calculated interaction energy confirmed the presence of strong interactions between the l-Cyst molecule and the resin particle. Elemental mapping, scanning electron microscopy (SEM), and scanning optical microscopy (SOM) images of the blended membranes represented a relatively uniform surface and particle distribution. Membrane water uptake and surface hydrophilicity were enhanced in the presence of l-Cyst. The blended membranes demonstrated high selectivity (> 99%), lower electrical resistance (< 5–6 Ω cm2), and better ionic permeability compared to the bare membrane. The blended membranes (HCEM–2.0 wt% l-Cyst) showed higher dialytic rate, lower energy consumption, and current efficiency in Pb2+ ion removal from water compared to the bare sample.