Stream microbial mats are dynamic communities of phototrophic and heterotrophic organisms that develop over intra-seasonal and inter-seasonal time scales. Diatom community composition is influenced by successional processes and physical and chemical gradients that together act to shape stream benthic habitats. In ephemeral streams of the McMurdo Dry Valleys (Antarctica, MCM LTER), previous work has demonstrated that in streams across the Fryxell Lake Basin, the diatom composition in microbial mat communities is determined largely by the annual and historical flow regime. However, this study examined broad trends in diatom community composition at the reach scale, which does not account for spatial variability within a stream reach. The goal of this study, therefore, is to examine the ecological responses of individual diatom species at finer spatial scales in order to more accurately interpret the general relationship between stream flow and microbial mat composition. Microbial mat samples were collected from two distinct mat types experiencing different flow regimes from 2 streams in the Fryxell Basin of Taylor Valley, MCM. Results show that spatial variation in microbial mats, which leads to variation in the frequency and duration of inundation by stream flow, plays an important role in determining diatom community composition. The relative abundances of endemic diatom species are higher in marginal mats that are less frequently inundated. Conversely, mats located within the stream channel experience more constant flow and have higher abundances of widespread diatom species. These results refine our current picture of diatom communities in Antarctic stream algal mats by appreciating the inherent variability within stream reaches in addition to reach-scale trends. A potential implication of these results is that with future climate changes leading to a warmer Antarctic continent, we expect to expand the suitable habitat for widespread diatom species and concurrently decrease suitable habitat for endemic diatom species, which could result in the reduction or loss of endemic species in these dynamic systems.