Selective separation of mono- and multi-valent ions has important applications in water reuse, desalination, and salt production. Innovative monovalent permselective cation-exchange membrane CR671 was developed by modifying the normal grade membrane CR67 with polyethyleneimine coating. Bench- and pilot-scale electrodialysis experiments were conducted at a brackish groundwater desalination facility to investigate desalination performance and ion selectivity using the CR671 and CR67 under different operating conditions. Both normal grade (CR67 and AR204) and selective (CR671 and AR112B) membranes achieved same desalting efficiency. Na-selectivity in terms of relative transport number using sodium as the standard ion was affected significantly by current density and linear velocity for the normal grade membranes while the selective membranes exhibited stable good Na-selectivity. The Na-selectivity of the CR671 was demonstrated up to 9 and 5 times better than the CR67 during pilot- and bench-scale electrodialysis, respectively. Hydraulic retention time and electrodialysis stack staging had minor impact on Na-selectivity at high current density. With the same hydraulic conditions, overall desalination behavior and ion selectivity were highly comparable between bench- and pilot-scale electrodialysis. It infers that bench-scale testing results can be used to simulate and project desalination performance and ion selectivity of pilot- and potentially full-scale electrodialysis applications.