High nitrate-nitrogen (NO3−–N) content is a typical feature of groundwater, which is the primary water source in the Kathmandu Valley, Nepal. Considering the Kathmandu Valley’s current problem of water scarcity, a user-friendly system for removing NO3−–N from groundwater is promptly desired. In this study, a simplified hydrogenotrophic denitrification (HD) reactor was developed for the Kathmandu Valley, and its effectiveness was evaluated by its ability to treat raw groundwater. The reactor operated for 157 days and showed stability and robustness. It had an average nitrogen removal efficiency of 80.9 ± 16.1%, and its nitrogen loading rate and nitrogen removal rate varied from 23.8 to 92.3 g–N/(m3∙d) and from 18.3 to 73.7 g–N/(m3∙d), respectively. Compared to previous HD reactors, this simplified HD reactor is a more user-friendly option for the Kathmandu Valley, as most of the materials used for the reactor were locally available and require less maintenance. The reactor is recommended for groundwater treatment at the household level. It has a current treatment capacity of 40 L/d, which can fulfill the daily requirements for drinking and cooking water in a household with 4–5 people.