Desert stream biota are subject to extremes in temperature and hyrdology. The gradient of water availability at a stream edge produces potential hotspots of microbial diversity and terrestrial-aquatic nutrient transfer. We investigated microbial communities and sediment biogeochemistry across this hydrologic margin in a cold and hot desert stream (Onyx River, McMurdo Dry Valleys, Victoria Land, Antarctica; Rio Salado, Sevilleta National Wildlife Refuge, New Mexico, USA). We used Denaturing Gradient Gel Electrophoresis and bacterial 16S rRNA clone libraries to characterize community composition and functional gene quantification and extracellular enzyme activities to characterize microbial nutrient cycling potentials. Sediment DIN and DOC availability is low at both sites (0.10-2.7 and 23.5-155 ug g dry soil^-1, respectively), with lower mean concentrations at Onyx River. Rio Salado sediments have higher potential organic matter breakdown rates. Nitrate correlates with conductivity at both sites (Pearson’s r = 0.51). Bacterial community compositional patterns across the physiochemical gradient are homogeneous and lower-diversity at Rio Salado and heterogeneous and higher-diversity at Onyx River. These differences may be linked to hydrologic variability and subsurface connectivity. This work illustrates the utility of molecular methods as tools for understanding controls on and biological responses to biogeochemistry in desert streams.