The choice of day roosts by microbats influences energetics, social interactions and breeding success. In Australia, the large-footed myotis (Myotis macropus) is dependent on waterways for foraging. However, the extent to which the species relies upon, and selects roosts within, riparian habitat is unknown. I studied the roosting behaviour of this species around a water reservoir near Melbourne, Victoria, during the summers from October 2002 to April 2005. I radio-tracked 31 bats to 17 tree roosts; colony size averaged 6.0 ± 1.6 bats and individuals used 1.3 ± 0.1 roosts during the tracking period (average 6.2 ± 0.6 days). Two roosts were also located in crevices in an old aqueduct tunnel, housing colonies of 10.8 ± 0.6 bats. Colonies emerged earlier from tunnel crevices (25.0 ± 3.6 min after sunset, range 6–53 min), compared with conspecifics in tree roosts (45.6 ± 2.1 min after sunset, range 10–83 min). Roost trees and cavities differed from available habitat trees and cavities in terms of smaller entrance areas to used (182.2 ± 49.3 cm2) versus unused (328.0 ± 61.8 cm2) cavities. The primary force driving roost selection by M. macropus appears to be proximity of suitable waterways for foraging. Retention and maintenance of extensive riparian habitat, as well as the preservation of other structures used for roosting, are the most important conservation strategies for management of the day-roosting habitat of M. macropus.