Despite the importance of microbes in ecosystem processes and the ubiquity of microbes in the environment, limitations of study techniques have left most microbial communities poorly described. In stream ecosystems, fungal and bacterial communities play critical roles in leaf decomposition, releasing energy and nutrients to higher trophic levels of the food web. This research examined microbial communities in Fossil Creek, a travertine stream in central Arizona. High and low quality leaf litter was placed in the creek at five study sites exhibiting heterogeneous environmental conditions (including differing stream morphology, water flow, water chemistry, and travertine deposition) to elucidate effects of litter quality and abiotic habitat characteristics on microbial community composition. Microbial communities colonizing decomposing leaves were characterized using terminal restriction fragment length polymorphism (TRFLP) analysis and clone library comparisons. Though leaf decomposition rates were strongly influenced by both litter quality and abiotic site characteristics, microbial communities were more strongly influenced by site. Bacterial and fungal community assemblages differed with incubation times: bacterial diversity and evenness increased from two days to one week, whereas fungal diversity and evenness decreased. Fungal community richness was negatively correlated with decomposition rates, suggesting a connection between microbial community structure and the ecosystem process of decomposition.