Nitrate contamination of groundwater has become a serious issue affecting the quality of drinking water and human health. An energy-efficient, low-cost, and simple reactor was developed to remove nitrate via hydrogenotrophic denitrification (HD). Hydrogen (H 2 ) supply was optimized by using a continuous supply of hydrogen (1-15 mL/min). The results revealed that the optimal condition was 5 mL/min, which yielded a nitrogen removal efficiency of 86.4% and a hydrogen effectiveness of 199 mg-N/g-H 2 . In the subsequent experiment, an intermittent hydrogen supply was used to improve the hydrogen effectiveness and hydrogen consumption. Using a cycle with a short period of hydrogen supply (3 min with hydrogen supply and 7 min with no hydrogen supply), excellent nitrogen removal efficiency (96.5%) was achieved, and the hydrogen effectiveness increased to 744 mg-N/g-H 2 . Furthermore, bacteria belonging to the Proteobacteria phylum and Betaproteobacteria class were the major components of the microbial community. However, Hydrogenophaga spp. (39.3%) was dominant under the continuous system, whereas Thauera spp. (58.5%) was the most abundant species under the intermittent system. In this study, Hydrogenophaga spp., Thauera spp., and Rhodocyclaceae, which were responsible for HD, afforded in efficient nitrogen removal from groundwater.