Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNAbased profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of two rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of sections through a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although the abundance of Mycobacterium was high, and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.