Recent research has focused on how small mammals persist in environments with high temporal unpredictability in the availability of resources. In areas such as the Australian arid zone, where irregular and unpredictable resource pulses drive small mammal population dynamics, some species persist through long periods of low resource availability in drought refuges. Refuges are small discrete areas in the landscape that provide a relatively consistent supply of resources for survival and reproduction throughout these low-resource times. We investigated the spatial scale and dynamics of populations of a threatened native rodent, the plains mouse Pseudomys australis, in cracking clay refuge habitat in central Australia during a period of low resource availability. Using live- and camera-trapping data collected over two years, and spatial modelling techniques, we assigned boundaries to the refuge areas and found that P. australis fluctuated both spatially and numerically over the study period, but stayed largely within the cracking clay refuge areas. Our research suggests that this refuge-using species is, for the most part, confined to cracking clay during periods of low resource availability and that this restricted habitat type forms the boundary of refuge areas. The assignment of boundaries, based on readily defined and spatially predictable landscape attributes, allows for more targeted and efficient management of these small areas to promote the persistence of this threatened species.