Microbial mats are common in polar streams and often dominate benthic biomass. Climate change may be enhancing the variability of stream flows in the Antarctic, but so far studies investigating mat responses to disturbance have been limited in this region. Mat regrowth was evaluated following disturbance by experimentally scouring rocks from an ephemeral McMurdo Dry Valley stream over two summers (2001–02 and 2012–13). Mats were sampled at the beginning and resampled at the end of the flow season. In 2012–13, mats were additionally resampled mid-season along with previously undisturbed controls. In 2001–02 rocks regained 47% of chlorophyll a and 40% of ash-free dry mass by the end of the summer, while in 2012–13 rocks regrew 18% and 27%, respectively. Mat stoichiometry differed between summers, and reflected differences in biomass and discharge. Oscillatoria spp. were greatest on scoured rocks and Phormidium spp. on undisturbed rocks. Small diatoms Humidophila and Fistulifera spp. increased throughout the summer in all mats, with the latter more abundant in scoured communities. Collectively, these data suggest that mats are variable intra-annually, responsive to hydrology and require multiple summers to regrow initial biomass once lost. These results will aid the interpretation of long-term data, as well as inform Antarctic Specially Managed Area protocols.