A bioelectrochemical system (BES) was designed to remove nitrate from groundwater with multiple barriers to prevent intrusion of undesired ions from its anolyte. Electric current was demonstrated to be a key force to transport nitrate ions, and OH⁻ ions were identified as a major competitor with nitrate for anion migration. The balanced mass between the lost nitrate fromgroundwater and the accumulated nitrate in the concentrating chamber suggested that nitrate removal was mostly due to physical migration, rather than biological reduction. Despite several challenges, the results encourage the further investigation and development of this BES for in situ nitrate remediation from groundwater.