Nitrate removal during anaerobic ammonium oxidation (anammox) treatment is a concern for optimization of the anammox process. This study demonstrated the applicability and long-term stability of the coupled anammox and hydrogenotrophic denitrification (CAHD) process as an alternative method for nitrate removal. Laboratory-scale fixed bed anammox reactors (FBR) supplied with H2 to support denitrification were operated under two types of synthetic water. The FBRs showed simultaneous NH4-N and NO3-N removal, indicating that the CAHD process can support NO3-N removal during the anammox process. Intermittent H2 supply (e.g. 5 mL/min for a 1-L reactor, 14/6-min on/off cycle) helped maintain the CAHD process without deteriorating its performance under long-term operation and resulted in a nitrogen removal rate of 0.21 kg-N/m3/d and ammonium, nitrate, and dissolved inorganic nitrogen removal efficiencies of 73.4%, 80.4%, and 77%, respectively. The microbial community structure related to the CAHD process was not influenced by changes in influent water quality, and included the anammox bacteria 'Candidatus Jettenia' and a Sulfuritalea hydrogenivorans-like species as the dominant bacteria even after long-term reactor operation, suggesting that these bacteria are key to the CAHD process. These results indicate that the CAHD process is a promising method for enhancing the efficiency of anammox process.