a Drinking water filters may be operated to promote or deter biological activity through upstream oxidant addition. While there are several water quality benefits from biofiltration, microbial growth in biofilters warrants further investigation. In this study, routine monitoring detected target DNA sequences for Naegleria fowleri in source water and Acanthamoeba spp. in source water and biofilter effluent, triggering further microbial community characterization. Full-scale anthracite and granular activated carbon (GAC) filters receiving chlorinated waters were compared in terms of effluent water quality (i.e., turbidity and particle counts), biological activity (i.e., adenosine triphosphate (ATP)), and the composition of the microbial community (i.e., 16S/18S rRNA gene sequencing, free-living amoeba). Because of rapid chlorine quenching by GAC, greater biomass development was observed in the GAC biofilter (ATP = 5 × 10 3 -5 × 10 4 pg cm −3 media) than the anthracite filter (ATP = 4 × 10 2 -1 × 10 3 pg cm −3 media). Due to possible sloughed biomass, GAC effluent also had consistently greater turbidity, particle counts, and cellular ATP than the anthracite filter. 16S rRNA gene sequencing revealed distinct taxonomic differences between the anthracite and GAC filters, and GAC also hosted a more diverse population (Shannon index: GAC = 3.7-5.0 and anthracite = 2.4-2.9). At the genus level, the anthracite filter contained mostly Undibacterium-like taxon (45-68%), while the GAC biofilter was dominated by Massilia (8-36%), Herbaspirillum (2-44%), and unknown Comamonadaceae (9-18%), among others. The presence of viable free-living amoebas was also detected in the GAC biofilter media. Further characterization of the eukaryotic 18S rRNA gene showed that anthracite predominantly harbored copepod Leptodiaptomus (67%), while a majority of the sequences in GAC are unknown.