Insectivorous bats make a significant contribution to mammalian diversity in central Australia, with 12 known extant species; however, little is known about their habitat preferences and how these interact with temporal patterns in their abundance and activity. Although most species forage widely and in a variety of habitats, we expected that woodlands associated with ephemeral rivers would constitute high-value habitat for bats because they provide tree hollows, suitable structural habitat for foraging, and canopies rich in invertebrate biomass. The aim of this research was to establish whether riparian woodlands were a focus of bat activity and to identify patterns in habitat use and whether these changed through time. We investigated the activity of bats in riparian woodlands and neighbouring vegetation over 2 years. Bat activity was higher in riparian woodland than in nearby vegetation, and this difference was most significant during a hot and dry summer. At the species level, body size and foraging guild were important factors explaining differences in activity, with larger 'open space' species more active in riparian woodland than adjacent habitat. In contrast, we did not detect significant differences in the activity of smaller vespertilionid species between habitats. Coinciding with patterns in invertebrate activity, bat activity was highest in summer and lowest in winter. Within river channels, canopy cover was important in explaining patterns in bat activity. There was also a significant location effect, with bat activity in some river systems much higher than in others. We propose that this is related to both regional variability in rainfall and productivity, in addition to topography. Our findings demonstrate the importance of riparian woodlands to bats in an arid environment, particularly during low-resource periods, and suggest that bats may be affected by future climate changes and degradation from fire impacts.