Acute disturbance and habitat heterogeneity at multiple scales produce environmental gradients that can alter animal community assembly through niche differentiation and extinction-colonisation processes. Over two years we sampled the taxonomic and functional diversity of terrestrial invertebrates (millipedes, ground beetles, spiders) inhabiting 28 river islands distributed across 4 river catchments. We hypothesised shifts in the activity density, species richness and functional diversity of invertebrate taxa related to disturbance from floods, island habitat heterogeneity and landscape structure. Specifically we predicted that the limited mobility of millipedes predisposed them to vulnerability to floods, whilst the diversity and abundance of predatory carabids and spiders, able to disperse aerially from source habitat, would be governed by island niche space and landscape structure. A combination of floods, island heterogeneity and landscape structure affected taxonomic and functional diversity. Increasing median flood peak decreased activity densities and rarefied species richness of millipedes and carabid activity densities, and increased spider activity densities. Landscape structure, local vegetation heterogeneity (e.g. tree cover, herbaceous plant cover) and geographic location also structured the activity density of all taxa and species richness of detritivorous millipedes. Island area was positively related to activity densities of predators, but species richness was unaffected. Functional diversity and trait dominance was structured by river catchment, indicating local trait pools, local habitat heterogeneity (herbaceous plant cover) and, for overwintering life stage and life-cycle timing, flood disturbance. Thus multiple processes (e.g. extinction-recolonisation, resource concentration) arising from combinations of flood disturbance, fine-scale habitat heterogeneity and wider landscape structure drive the taxonomic and functional assembly of these island communities.