Microinvertebrates play a critical role in riverine food webs, and recent studies have hypothesized that slackwaters, non-flowing regions associated with the main channel, are important for their reproduction and recruitment. However, little is known regarding the population and community dynamics of microinvertebrate communities in slackwater regions, or how they compare with those in mid-channel regions. This study examined microinvertebrate communities in the epibenthic and pelagic zones of slackwater and mid-channel regions (i.e. four habitats) of an Australian floodplain river in relation to physico-chemical parameters and food availability (as estimated by chlorophyll-a concentration) between September 2005 and November 2006. Results from this study indicate that microinvertebrate abundance and diversity were greater in slackwater habitats than mid-channel habitats overall, corresponding with the slower current velocities associated with the former. Nevertheless, communities in all four habitats were most abundant and diverse in late spring (coinciding with an increase in water temperature), and followed similar seasonal trajectories in terms of density, taxon richness and community structure. These findings support the view that slackwaters are important for in-channel microinvertebrate production, and suggest that animals frequently disperse (either actively or passively) among slackwater and other main channel regions year round. Given the critical importance of microinvertebrates in riverine food webs, rivers should be managed with a view to maintaining a natural variety of accessible slackwater regions in order to support the production and survival of microinvertebrate communities.