Drinking Water Treatment Plants employ biofiltration systems to increase water quality through nutrient reduction. Microbial biofilms housed in biofilter media, are responsible for nutrient uptake and biodegradation. The purpose of this study was to re-evaluate the function and efficiency of biofilter media and investigate seasonal changes in the microbial populations. TOC and DO were more reduced in Granular Activated Carbon (GAC) media than in anthracite. Heterotrophic plate counts (HPC) were conducted to establish seasonal trends on microbial population. PCR-amplified 16S rRNA fragments were sequenced to compare microbial communities. Summer samples have higher HPC than winter samples. Summer samples yielded a reduction in microbial diversity and no detectable overlap with winter samples. Confocal microscopy conducted to qualitatively visualize the structure of biofilms was complemented by quantitative COMSTAT analysis showing GAC with double the biomass due to a greater level of attachment sites. GAC outcompetes anthracite in chemical adsorption and biological activity.