Stormwater retention ponds are ubiquitous in urban and suburban landscapes of the United States. Most studies of the microbiology of these ponds have focused on the abundance and removal efficiency of fecal indicator bacteria. Here we provide the first comprehensive study of microbial community diversity and activity in these ponds, and assess how different environmental and engineering factors influence these communities. Watershed land-use had no grouping effect on pond geochemistry or biology. Instead, we found that microbial community composition and activity were best explained by site-specific environmental variables. 16S rRNA gene sequence analysis indicated that bacterial community structure varied greatly across sampled ponds, and appeared to be the result of autochthonous bacterial growth and not simply surface runoff. Metagenomic sequencing of pond viral communities suggested that viral taxa were influenced by external inputs, with viromes composed of bacteriophage that infect environmental bacteria, as well as viruses that infect eukaryotes and phages that infect bacteria pathogenic to eukaryotes. Collectively, our results indicate that the environmental conditions and microbial communities of these ponds vary greatly, even among ponds in close spatial proximity, and that pond microbial communities appear to be shaped by site-specific environmental factors.