The microbiological quality of drinking water has aroused increasing attention due to potential public health risks. Knowledge of the bacterial ecology in the effluents of drinking water treatment units will be of practical importance. However, the bacterial community in the effluents of drinking water filters remains poorly understood. The changes of the density of viable heterotrophic bacteria and bacterial populations through a pilot-scale drinking water treatment process were investigated using heterotrophic plate counts and clone library analysis, respectively. The pilot-scale treatment process was composed of preozonation, rapid mixing, flocculation, sedimentation, sand filtration postozonation, and biological activated carbon (BAC) filtration. The results indicated that heterotrophic plate counts decreased dramatically through the drinking water treatment processes. Clone library analysis indicated the significant change of bacterial community structure through the water treatment processes. Betaproteobacteria was dominant in raw water, the sand filter effluent and the BAC filter effluent. This work could provide some new insights on drinking water microbial ecology.