Wafer-enhanced electrodeionization (WE-EDI) is an electrically driven separations technology that occurs under the influence of an applied electric field and heavily depends on ion exchange resin chemistry. Unlike filtration processes, WE-EDI can be used to selectively remove ions even from high concentration systems. Because every excess ion transported increases the operating costs, the selective separation offered by WE-EDI can provide a more energy-efficient and cost-effective process, especially for highly concentrated salt solutions. This work reports the performance comparison of four commonly used cation exchange resins (Amberlite IR120 Na+, Amberlite IRP 69, Dowex MAC 3 H+, and Amberlite CG 50) and their influence on the current efficiency and selectivity for the removal of cations from a highly concentrated salt stream. The current efficiencies were high for all the resin types studied. Results also revealed that weak cation exchange resins favor the transport of the monovalent ion (Na+) while strong cation exchange resins either had no strong preference or preferred to transport the divalent ions (Ca2+ and Mg2+). Moreover, the strong cation exchange resins in powder form generally performed better in wafers than those in the bead form for the selective removal of divalent ions (selectivity > 1). To further understand the impact of particle size, resins in the bead form were ground into a powder. After grinding the strong cation resins displayed similar behavior (more consistent current efficiency and preference for transporting divalent ions) to the strong cation resins in powder form. This indicates the importance of resin size in the performance of wafers.