Biological activated carbon (BAC) filtration can usually perform well in removal of biodegradable organic compounds in drinking waters. In this study, a pilot-scale down-flow BAC filtration system was constructed for treatment of ozonated waters. The changes of biomass concentration and bacterial community in the BAC filters with contact time and service time were characterized using phospholipid fatty acid (PLFA) analysis and 16S rRNA gene clone library analysis, respectively. The operational results indicated the BAC filtration system could effectively remove dissolved organic carbon (DOC) and assimilable organic carbon (AOC). Biomass concentration decreased with contact time, but showed only a slight change with service time. Contact time and service time could affect the microbial community structure. Alphaproteobacteria was the largest bacterial group and might have important links with the DOC and AOC removal. This work might provide some new insights into microbial community and biological process in the drinking water biofilters. (C) 2012 Elsevier Ltd. All rights reserved.