The treatment performance and spatial microbial community structure of three parallel denitrifying biological filters (DNBFs) operated with methanol, ethanol and acetate, respectively, were explored. The acetate-fed DNBF presented the highest denitrification rate and NOx-N (NO2-N and NO3-N) removal efficiency, while the methanol-fed DNBF showed the lowest carbon consumption and NOx-N removal efficiency. Distinct spatial distribution patterns of terminal restriction fragment length polymorphism fingerprints were observed among the DNBFs. The ethanol enhanced captured biofilms throughout the flowpath of DNBF had the highest diversity and evenness. The methanol-enhanced attached biofilm along the flowpath presented the highest evenness, but lowest richness and limited diversity. β-Proteobacteria was dominant in the microbial community in all of methanol, ethanol and acetate enhanced biofilm; however, different external carbon sources resulted in different dominant genera species. Thauera was dominant in the acetate enhanced bacterial community, while both Dechloromonas and Thauera were dominant in that of ethanol fed. However, methylotrophic bacteria (Methyloversatilis and Methylotenera) dominated exclusively in the methanol enhanced bacterial community throughout of the DNBF.