Caridean shrimps are an important component of lowland river ecosystems and their distributions may be affected by river regulation. We studied the mesoscale distributions of Paratya australiensis, Caridina mccullochi and Macrobrachium australiense in five lowland rivers of the Murray–Darling Basin, south-eastern Australia. We distinguished habitat patches according to water-current velocity and channel location – still littoral (SL), slow-current-velocity littoral (SCVL) and moderate-current-velocity channel (MCVC) – and investigated ontogenetic shifts in habitat use. We sampled seven reaches for shrimp in March 2003 and December 2003 using a modified backpack electrofisher. Paratya australiensis occurred in all habitats but was mostly associated with SL. All life stages of C. mccullochi utilised SL and SCVL, and only a few adults were collected from areas with greater than slow current velocity. The habitat preference of M. australiense changed with development: larvae only occurred in SL, but adults and berried females strongly preferred MCVC. Low flows and slow water currents are characteristic of lowland rivers in southern Australia during summer and autumn (December–April), the period during which shrimps’ larval development and juvenile recruitment occurs. Caridina mccullochi and M. australiense may rely on still and slow-current-velocity habitats during larval development and juvenile recruitment and to facilitate upstream movements.