Bacterial communities in biofilters can improve drinking water quality through the biodegradation of dissolved contaminants but also pose potential risks by harboring and shedding microbes into the drinking water distribution system. In this study, pilot-scale granular activated carbon (GAC)-sand and anthracite-sand pilot-scale biofilters were investigated to determine the effects of filter design and operation on the microbiome of the filter media and its relationship to the microbiome in the filter effluent water. Bacterial abundance in the biofilters was relatively stable over time. Bacterial community composition exhibited spatial variation (i.e., with bed depth) and temporal variation linked to water quality changes. Bacterial community composition was significantly affected by the media type (GAC vs anthracite) and backwashing strategy (chloraminated water vs nonchloraminated water). The biofilters reduced bacterial abundance in the water (∼70%) but had only a minor effect on the bacterial community composition in the filtrate. Overall, our results suggest that the bacterial communities growing on biofilters affect filtered water quality primarily through the biotransformation of pollutants and nutrients rather than by altering the microbial community composition of the water as it passes through the filter.