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 (S-0) disproportionation due to the increase of the contact time between water and S-0 particle. The H+ generated from S-compartment could be reduced as H-2 by electrochemical process in H-compartment, and the generated H-2 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 variatioris were found in the microbial community at different locations of the combined reactor. (C) 2015 Elsevier B.V. All rights reserved.