Assessments of groundwater aquifers made around the world show that in many cases, nitrate concentrations exceed the safe drinking water threshold. This study assessed how bioelectrochemical systems could be used to enhance nitrate removal from waters with low organic carbon concentrations. A two-chamber microbial electrosynthesis cell (MES) was constructed and operated for 45 days with inoculum that was taken from a municipal wastewater treatment plant. A study showed that MES can be used to enhance nitrate removal efficiency from 3.66% day−1 in a control reactor to 8.54% day−1 in the MES reactor, if a cathode is able to act as an electron donor for autotrophic denitrifying bacteria or there is reducing oxygen in a cathodic chamber to favor denitrification. In the MES, greenhouse gas emissions were also lower compared to the control. Nitrous oxide average fluxes were −639.59 and −9.15 µg N m−2 h−1 for the MES and control, respectively, and the average carbon dioxide fluxes were −5.28 and 43.80 mg C m−2 h−1, respectively. The current density correlated significantly with the dissolved oxygen concentration, indicating that it is essential to keep the dissolved oxygen concentration in the cathode chamber as low as possible, not only to suppress oxygen’s inhibiting effect on denitrification but also to achieve better power efficiency.