Interactions between flow regime, sediment dynamics and benthic invertebrates have seldom been studied in rivers experiencing naturally high suspended sediment loads. This paper examines invertebrate responses to hydrological and sedimentary processes over an annual cycle in a morphologically heterogeneous reach of a river that receives large volumes of fine sediment. Flow regime and sedimentary conditions showed a marked seasonal pattern, with fine sediment accumulating during low flows and after small flood events and not being removed until the large floods that occurred in autumn. The magnitude of sediment accumulation differed between habitats (e.g. being greater in pools than in riffles). The turnover in invertebrate assemblages, measured as beta diversity, was greatest in winter and decreased during summer as deposited fine sediment accumulated across the reach, suggesting that observed patterns of turnover were influenced by seasonal and habitat-specific rates of sedimentation. Some of the spatial and temporal patterns in invertebrate assemblages were subtle, complex and difficult to interpret, but co-inertia analysis indicated an overriding influence of low flows and associated sedimentation on their composition. Floods capable of entraining coarser bed material, along with smaller events accompanied by extensive mobilization of fine sediment, also influenced assemblages and resulted in immediate changes to assemblage composition and abundance. Assemblages appeared to exhibit resilience over the timescale of the study, with similar assemblages found at the beginning and at the end of the study period. Copyright © 2013 John Wiley & Sons, Ltd.