Terrestrial arthropods form biodiverse communities that support the structure and functioning of riparian ecosystems, and are shaped by local to large-scale connectivity in three dimensions. In particular, river characteristics such as size and flow permanence are likely to influence lateral cross-channel connectivity, but how such temporally variable natural barriers shape riparian communities is rarely quantified. We tested the connectivity of communities comprising a diverse family of largely ground-dwelling terrestrial arthropods (ground beetles, Coleoptera: Carabidae) by repeatedly sampling parallel riparian zones along rivers spanning a gradient of flow permanence during flow recession—when declining water levels theoretically reduced the barrier separating communities on left and right banks. We quantified cross-channel connectivity by comparing left–right bank community dissimilarity using Sørensen β diversity and null-model-derived z-scores, distinguishing species capable of flight from those with limited or no flight ability. Communities in parallel riparian zones were similar along the gradient, suggesting that river channels represent comparably weak barriers to cross-channel movement regardless of water levels. In particular, species capable of flight were unaffected by in-channel conditions, whereas the cross-channel comparability of assemblages with limited flight abilities increased as the flow declined. The replacement of water-associated species by generalists as flow declined suggests that access to water as a resource may be more important than the barrier posed by water in structuring riparian ground beetle communities. To balance access to key resources, such as water, with the connectivity communities require for long-term resilience, management actions should seek to mitigate climate-driven shifts in the spatiotemporal extent of river drying.