Abstract The removal of perchlorate (ClO4−) and nitrate (NO3−) from drinking water was investigated in a combined reactor of sulfur autotrophy (S-compartment) and electrochemical hydrogen autotrophy (H-compartment). The removal efficiencies of NO3− and ClO4− in the S-compartment and H-compartment were affected by hydraulic retention time (HRT) and current intensity, respectively. The sulfur- and hydrogen-autotrophic denitrifying process favored over the process of sulfur- and hydrogen-autotrophic perchlorate reduction in the combined reactor. The longer HRT could lead to sulfur (S0) disproportionation due to the increase of the contact time between water and S0 particle. The H+ generated from S-compartment could be reduced as H2 by electrochemical process in H-compartment, and the generated H2 as an electron donor was utilized to reduce NO3− and ClO4− by hydrogen autotrophic reduction. The oxidation reduction potential (ORP) in the effluent from S-compartment and H-compartment were below −180 mV, suggesting good anaerobic conditions for the reduction of NO3− and ClO4− in the combined reactor. Some sulfur- and hydrogen-autotrophic denitrifying bacteria could use both NO3− and ClO4− as electron acceptors in the combined reactor. The DGGR profile illustrated that some variations were found in the microbial community at different locations of the combined reactor.