Caridean shrimp have considerable effects on ecosystem processes and, thus, understanding their use of key habitats is important for determining their potential ecological effect. The present study examined the meso-habitat use of Macrobrachium spinipes, a large-bodied and important amphidromous species, in the Daly River, northern Australia. We examined shrimp abundance at four common meso-habitat types; sand bank, rock bars, undercut and structurally complex banks and mid-channel areas at five sites on three occasions during the dry season (May to October). We found that habitat use changed considerably first, with ontogeny, and, second, with the colonisation of habitats with algae and macrophytes as the dry season progressed. As juveniles, their habitat use was strongly associated with well structured bank environments early in the dry season. By the mid-dry season, juveniles were more abundant within sand habitats recently colonised with macrophytes and filamentous algae. Females showed little change in habitat use, whereas large-bodied dominant males generally favoured rock bars and heavily structured bank environments. The present study has provided significant insights into the changes in use of key riverine habitats throughout the dry season by an ecologically important species. This information will be of considerable value to the determination of environmental flow requirements and food-web investigations.