The ecological impacts of introduced species can reveal mechanisms underlying habitat selection and behaviour. We investigated the habitat use of native frog species and the invasive cane toads (Rhinella marina) in tropical northern Australia to measure overlap in habitat use, and to test if the presence of the cane toad influences frog behaviour. Native frog species and the cane toad both preferred habitats close to water and unvegetated holes. However, native frogs were found further from water (on average 19.4 m) than were toads (on average 12.6 m), and preferred areas with higher vegetation (8–50 cm) than did toads, which were more abundant in vegetation lower than 8 cm. For both types of anuran, the next neighbour was more often of the same type (89% in frogs, 52% in toads) than expected by chance (observed ratio: 75% frogs vs 25% toads), reflecting these differences in habitat use. Our counts of frog abundance increased on average 14.5% in areas from which we removed cane toads temporarily. This result suggests that cane toads inhibit the activity of native anurans either by inducing avoidance, or by reducing activity. By modifying the behaviour and spatial distribution of native taxa, invasive cane toads may curtail activities such as feeding and breeding.