Understanding ecological consequences of climate change is critically important but difficult, because changes include environmental warming as well as alterations to hydrology and biogeochemistry and interactions with other stressors. In river systems dormant aquatic invertebrates remain viable in riverbed sediment during dry phases, forming a source for recolonisation during wet periods. The likely impacts of climate change on the viability of this recolonisation source remains poorly known, due to the complexity of effects. We used a microcosm experiment with a simple warming treatment to look at the interactive effects of warmer and drier conditions on river invertebrate diversity in isolation. Extended drying and increased temperatures had a negative effect on diversity and shifted assemblage composition, particularly for temperate rivers, despite rivers in semi-arid regions sampled having similar hydroperiods. There was no interactive effect of warming and extended drying on invertebrates, despite a negative effect on sediment moisture. Semi-arid rivers had higher potential for dry riverbeds to act as a source for recolonisation under climate change, given high resistance of invertebrate assemblages in sediment with low moisture levels and elevated temperatures. Regardless of the complexity of real world interactions and difficulties scaling microcosm experiments, regional differences in response to climate stressors allows prediction of differing limits to adaptation.