In intermittent desert streams, connectivity between surface water and ground water is especially important to biological activity, with an often large hyporheic zone contribution to transient storage and stream nutrient cycling. The positive relationship between nutrient retention and transient storage is established, but microbial ecology of hyporheic sediments is understudied, aside from at the process level. Stream and microbial ecologists, aided by molecular techniques, have recently documented differences in stream microbial communities related to nutrient chemistry, season or water source. In this study, we measured bacterial community composition and biogeochemical parameters from surface and hyporheic waters through study reaches of six desert streams, using samples collected in conjunction with whole-stream 15NO3 injection experiments. Between streams, bacterial diversity and heterogeneity were strongly related to the hydrological retention factor of each reach and nitrate uptake rates. Within streams, bacterial community structure differed between surface and ground water habitats and was related to well-specific nitrate uptake. There is a positive relationship between surface water - ground water interaction and microbial diversity in these desert streams; loss of hydrologic connectivity due to climate change or anthropogenic engineering could diminish not only stream function but biotic diversity at the microbial level.