Littoral habitats in large rivers are influenced to varying degrees by changes in discharge. Irrigation abstractions can increase the amount of habitat that would naturally be dewatered during low flow periods and therefore it is important to have some knowledge of the potential impact this may have on riverine macroinvertebrates. The macroinvertebrate assemblages of common littoral habitats in riffles, pools and runs in two reaches each of the Macquarie and Mersey Rivers, northern Tasmania, Australia were compared from samples collected during the low flow and irrigation season, between December 1991 and April 1992. The area under water of these habitats, riffle substrata, macrophyte beds and coarse woody debris, responded differently to changes in discharge. Within a reach, the same taxonomic groups often dominated the total number of macroinvertebrates for all habitats, but there were differences in the proportions contributed by these taxa to the different habitats. In general, taxa characteristic of slow‐flowing or lentic habitats, such as ostracods and amphipods, were dominant in macrophyte beds in pools and runs, whereas taxa such as larval elmid beetles and hydropsychid caddisflies were dominant in riffles. A substantial component of the fauna from each habitat within a reach was unique to that habitat, but there was always a similar number of taxa common to all habitats. Classification and ordination grouped samples from both rivers firstly by habitat and secondly by month and reach. Total density and family richness of invertebrates differed by reach, habitat and month in both rivers, except for richness in the Mersey River where habitat was not significant. Differences in densities and numbers of invertebrate families among habitats were not consistent between reaches for each river. This study has highlighted the differences in macroinvertebrate assemblages of several littoral habitats in two lowland rivers in Tasmania. Differences in taxonomic composition, density and richness among habitats within reaches strongly imply the uniqueness of these habitats in terms of the invertebrate faunas that occupy them. We suggest that if maintenance of biotic diversity is an aim of instream flow management, water allocations that address low flows should place a high priority on the maintenance of a diversity of habitats.