Summary Drought disturbances can have strong but variable effects on aquatic communities and little is understood about the impacts of drought, fragmentation and habitat reconnectivity on the dynamics of intermittent stream fish metacommunities. We performed two experiments using outdoor stream mesocosms to test the effects of drought‐mediated connectivity and habitat heterogeneity on realistic stream fish assemblages at local (pool/patch) and regional (stream unit) scales under non‐drought versus drought conditions (Exp1) and under drought conditions with ‘pulse’ flow connectivity versus ‘non‐pulse’ (Exp2). Survivorship, ‐diversity and γ‐diversity differed little at the unit level between treatments and experiments, but significant interactions between treatments and pool position were observed for species richness and abundances at the pool‐level. Specifically, drought (Exp1) and non‐pulse (Exp2) treatments had consistently higher species richness and abundances in deeper downstream pools due to downstream‐biased immigration during the onset of drought and higher residency among fishes in downstream pools. Species‐specific responses in these treatments resulted in downstream pools that were characterised by species pre‐adapted to lentic conditions (e.g. sunfishes), whereas upstream pools were characterised by smaller‐bodied top‐water and pelagic species. Non‐drought (Exp1) and pulse (Exp2) treatments showed no difference in richness or abundances among pool positions and assemblages were generally well‐mixed, indicating that connectivity (even a brief pulse) of pool refugia was important for determining local and regional assemblage structure and mediating the impacts of drought. These experiments demonstrate that stream fish assemblages responded strongly to reduced flows and fragmentation, and that metacommunity dynamics were structured by differential emigration and immigration rates and directionality among heterogeneous and variably connected pool habitats.