Bacterial diversity, based on 16S rRNA gene sequencing, was compared in paired water and adjacent air masses in an urban center. Diversity patterns are evaluated in comparison to non-urban air and water, as well as to physical factors in the urban environment. The influence of pollution sources, including sewage contamination, on taxonomic distributions are also considered in both air and water. This study provides insight into the microbiome of the urban environment and the multidirectional exchange patterns influencing microbial biogeography in the urban environment.