Electrochemical reduction with a flow-through electrode system (FES) has been regarded as an effective method for water decontamination. However, under a direct voltage (DV) power supply, the reduction efficiencies were strongly limited by the gas bubbles generated in porous electrodes and the electrostatic repulsion between the negatively charged pollutants and cathode. Herein, square-wave alternating voltages (SWAV) were applied to regulate the anodic−cathodic polarities of electrodes for eliminating the gas accumulation in porous electrodes and enhancing the mass transfer efficiency. Under the optimized SWAV parameters, the Cr(VI) reduction and energy efficiency were increased obviously to ∼86 and 84% as compared with the 20%−30% Cr(VI) reduction and 30%−50% energy efficiency under the DV power supply. With periodically altering the anode to cathode, localized H + and Cr(VI) species were formed on the anodic interface via H 2 O oxidation and Cr(VI) adsorption, which were further in situ reduced for enhancing the Cr(VI) mass transfer and reduction efficiencies. In addition, O 2 species generated via H 2 O oxidation was also in situ reduced to H 2 O 2 species, hence promoting the Cr(VI) reduction and operation stability for most Cr(VI) reduction with a stable energy efficiency (∼82%) over a 10 day operation (8 mg/L Cr(VI) and 500 L/m 2 /h flux). The successful application of SWAV may derive similar decontamination strategies, especially for electrically charged pollutants with the H + or OH − ions as reactants.