The McMurdo Dry Valley lakes are the closest analog on Earth to extraterrestrial environments that may harbor life. Phylogenetic analysis of its bacterial communities offers insight into the origins of life and its evolution. In this study, we determined the bacterial community composition throughout the water column of the McMurdo Dry Valley lakes. While these bacterial communities were largely stable on an inter-annual basis, the spatial patterns in bacterial diversity were strongly linked with physical and chemical gradients in the lakes, indicating that bacterial activity modulates ecosystem function in extreme environments. Investigation of acetate and glucose utilizers in the McMurdo Dry Valley lakes imply that even minor components of the overall bacterial community may play important roles in the nutrient cycling of these lakes.