A large number of permanent and temporary wetlands are associated with the lowland rivers in south-eastern Australia. Regulation of these rivers for irrigated agriculture has probably increased the temporary nature of some wetlands because the reduced frequency of overbank flows causes them to remain dry for longer. The responses of macroinvertebrate assemblages (species composition and abundance) to inundation in permanent and temporary wetlands on the floodplain of the unregulated Ovens River were examined, and these responses were compared with those from permanent and temporary wetlands in the Barmah-Millewa forest of the regulated River Murray. The compositions of macroinvertebrate assemblages in permanent wetlands could not be distinguished from those of temporary wetlands on the Ovens after inundation, although changes in abundance of some taxa (especially chironomids) meant that the assemblages in permanent wetlands differed significantly before and after flooding. In contrast, after inundation, permanent and temporary wetlands in the Barmah-Millewa forest differed significantly and this difference was sustained through time. This different response of macroinvertebrate assemblages on the two floodplains may be an effect of regulation, although other explanations, such as differences between the floodplains in the mechanism of inundation and historical water regimes, or climatic differences between years, may also be important. Further studies should include concurrent sampling on a wider range of regulated floodplains and experiments manipulating water allocations to wetlands, to test specific hypotheses about the effects of water regime on biota.