Nitrates in different surface and groundwater resources became a worldwide problem which raised concerns due to severe impacts on human and animal health. Although diverse abiotic methods are reported to remove nitrate from water, they fail to entirely treat nitrate. Biological denitrification is the only treatment method capable to reduce inorganic nitrate compounds to harmless nitrogen gas. Autohydrogenotrophic denitrifiers were applied in this study to prevent any problematic outcomes of heterotrophs’ metabolisms raised from organic carbon source. A novel upflow bio–electrochemical reactor (UBER) was designed and employed to generate in-situ hydrogen and fulfill denitrifying process at cathode zone. Granular activated carbon (GAC) utilized to play a dual role as biocarrier and cathode material. Simple but effective design of this reactor helped to cope with problematic phenomenon of accumulation of nitrite through optimization of electric current (I), Hydraulic retention time (HRT), and recycle ratio. Moreover, the developed models helped to attain a proper optimization for the aforementioned operating factors.