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The environmental factors that determine species richness and community structure in running waters have long been studied, but how these factors hierarchically and/or interactively influence benthic communities remains unclear. To address this research gap, we identified the principal abiotic factors that determine the taxonomic composition and functionality of stream macroinvertebrate communities and explored possible hierarchical and/or interactive patterns. We analyzed a large dataset from Greek rivers, and compared multiple macroinvertebrate metrics and traits between perennial and intermittent watercourses during wet and dry periods. We found that macroinvertebrates were primarily influenced by two ecological gradients: (i) aquatic vegetation-conductivity; and (ii) water temperature-canopy cover. Macroinvertebrates in perennial rivers were mainly influenced by the first gradient, whereas in intermittent rivers both gradients were important. Taxonomic richness and diversity were higher and temporally stable within years in perennial rivers, whereas in intermittent rivers, these metrics peaked during early summer, before the onset of streambed desiccation. The two environmental gradients determined the taxonomic richness and diversity in both spring and summer; however, a clear influence of hydrological factors (wetted width, water depth, flow velocity and discharge) was observed only in the intermittent samples. We conclude that the benthic invertebrate taxonomic richness and diversity in highly variable environments is primarily determined by hydrological variation and ultimately fine-tuned by local habitat factors. As climate change scenarios predict severe modification of hydrological and local habitat factors, this study concludes that in river management, hydrological restoration should be prioritized over other local habitat factors by maintaining natural hydrological variability, to ensure aquatic community richness and diversity. (c) 2019 Elsevier B.V. All rights reserved.