The ecology of the dusky hopping mouse (Notomys fuscus) was studied at Pelican Waterhole in south-west Queensland and Montecollina Bore in north-east South Australia over an eight-year period. Population parameters of N. fuscus differed markedly between the two study sites. Whilst the population at Montecollina Bore exhibited large fluctuations in size, captures at Pelican Waterhole were lower but more consistent. Recaptures between sessions at Montecollina Bore peaked at 60% but no individuals were recaptured at Pelican Waterhole. No evidence of seasonal breeding was recorded at either site. Male N. fuscus captured at Montecollina Bore were significantly heavier (average 31.4 g) than Pelican Waterhole animals (average 26.6 g). Over a 1–4-night period, the maximum linear distance moved by radio-collared individuals was 1.5 km (average 481 m) at Pelican Waterhole and 400 m (average 199 m) at Montecollina Bore. Differences in population dynamics between the two sites are ascribed to food availability and habitat quality. Whilst Pelican Waterhole may constitute a more stable, less degraded environment, Montecollina Bore appears to be defined by periods of either very high or very low resource availability depending on rainfall. The abundance of dingoes and low cat and fox activity may contribute to the persistence of N. fuscus at the two study sites.