Understanding how natural disturbance regimes drive biodiversity patterns is a major research challenge. Disturbances disrupt local communities by increasing population mortality and alter dispersal between communities. Yet, how species’ ecological strategies and disturbance regimes intertwine to shape the structure of metacommunities across space and time remains poorly understood. Drying river networks (DRNs) exemplify ecosystems structured by natural disturbances: drying events disrupt both local habitat within reaches and connectivity among flowing sections. Drying-wetting cycles thus alter two major mechanisms shaping metacommunity diversity: ecological drift and dispersal dynamics. In this study, we present a mechanistic metacommunity model that simulates species’ ability to withstand drying in place (resistance strategy) and to recolonize communities after rewetting (resilience strategy). Coupling this model with realistic hydrological models, we simulated community dynamics in four European DRNs encompassing variable flow intermittence regimes. Our aim was to investigate the relative importance of flow intermittence, network connectivity and species’ ecological strategies in shaping spatio-temporal biodiversity patterns. We show that higher connectivity increases reach-level α-diversity and decreases reach-level temporal β-diversity, whereas flow intermittence has the opposite effects. At the metacommunity scale, more intermittent DRNs exhibited low mean α-diversity and high spatial β-diversity, while DRNs with downstream drying exhibited high temporal β-diversity. Finally, we show that high levels of species drying resistance and dispersal counteract the effect of flow intermittence, leading to high mean α-diversity and low spatial and temporal β-diversities at the metacommunity scale. In contrast, maximal dispersal distance had complex, non-linear effects on spatial and temporal β-diversities, because dispersal amplifies both community stochasticity and biotic homogenisation. Altogether, our work emphasises how stochastic recolonisation of disturbed communities and biotic homogenisation interact with species resilience and resistance strategies to shape the spatio-temporal structure of biodiversity.