SUMMARY1. We compared aquatic macroinvertebrate assemblage composition within and between habitats (pools and riffles) at four sites on two intermittent streams in Victoria, Australia during a drought year followed by a wetter year to see how different spatial and temporal scales influenced patterns of community structure detected by multivariate techniques of ordination and classification. We also examined the fit between faunal groups and ‘flow phases’ characterized by multivariate analyses of physicochemical variables in an earlier paper.2. Pools contained more taxa and individuals than riffles. At the more temporary site, there was considerable overlap between the faunal composition of pools and riffles, whereas habitat‐specific assemblages consistently occurred at the more permanent sites. Most taxa were either tolerant, permanent stream forms able to persist in streams that dry briefly, or facultative species that occur in lotic or lentic habitats. Few species appeared specifically adapted to temporary waters.3. Within habitats, there were some matches between faunal groups and flow phases, especially with the onset of the ‘diminishing flow’ phase, characterized by rising water temperature and conductivity, and declining pH and dissolved oxygen. However, disjunctions among faunal groups were less marked than those between flow phases, and were absent at an intermediate scale when habitats were pooled within sites. At the broadest scale of analysis (within habitats between sites and years), historical events (e.g. whether pools upstream dried completely during the previous summer) apparently influenced community composition as much as site‐specific abiotic