Diatoms are diverse and widespread freshwater Eukaryotes that make excellent microbial subjects for addressing questions in metacommunity ecology. In the McMurdo Dry Valleys of Antarctica, the simple trophic structure of glacier-fed streams provides an ideal outdoor laboratory where well-described diatom assemblages are found within two cyanobacterial mat types, which occupy different habitats and vary in coverage within and among streams. Specifically, black mats ofNostocspp. occur in marginal wetted habitats, and orange mats (Oscillatoriaspp. andPhormidiumspp.) occur in areas of consistent stream flow. Despite their importance as bioindicators for changing environmental conditions, the role of dispersal in structuring dry valley diatom metacommunities remains unclear. Here, we use MCSim, a spatially explicit metacommunity simulation package for R, to test alternative hypotheses about the roles of dispersal and species sorting in maintaining the biodiversity of diatom assemblages residing in black and orange mats. The spatial distribution and patchiness of cyanobacterial mat habitats was characterized by remote imagery of the Lake Fryxell sub-catchment in Taylor Valley. The available species pool for diatom metacommunity simulation scenarios was informed by the Antarctic Freshwater Diatoms Database, maintained by the McMurdo Dry Valleys Long Term Ecological Research program. We used simulation outcomes to test the plausibility of alternative community assembly hypotheses to explain empirically observed patterns of freshwater diatom biodiversity in the long-term record. The most plausible simulation scenarios suggest species sorting by environmental filters, alone, was not sufficient to maintain biodiversity in the Fryxell Basin diatom metacommunity. The most plausible scenarios included either (1) neutral models with different immigration rates for diatoms in orange and black mats or (2) species sorting by a relatively weak environmental filter, such that dispersal dynamics also influenced diatom community assembly, but there was not such a strong disparity in immigration rates between mat types. The results point to the importance of dispersal for understanding current and future biodiversity patterns for diatoms in this ecosystem, and more generally, provide further evidence that metacommunity theory is a useful framework for testing hypotheses about microbial community assembly.