In a context of increasing landscape modifications and climatic changes, scale hierarchy becomes an ever more crucial issue to integrate in the analysis of drivers and stressors of biological communities, especially in river networks. To cope with this issue, we developed (i) spatial hierarchical models of functional diversity of stream invertebrate communities to assess the relative influence of local- vs. regional-scale factors in structuring community assembly, and (ii) analysis of metacommunity elements to determine the ecological processes behind the structuring. The spatial structuring of benthic invertebrate communities was investigated over 568 sites in South-eastern France. Community structure was mainly driven by the altitudinal gradient and spring flow variation at broad scales, with functional diversity gradually decreasing with elevation and being maximized at intermediate levels of flow variability. According to the ‘elements of metacommunity structure’ analysis, the prevailing influence of the altitudinal gradient was also supported by a Clementsian structuration of invertebrate communities. Conversely, the influence of observed climatic changes in temperature and rainfall was weak and observed only at fine scales. As a result, natural environmental filters were stronger drivers of the functional diversity of communities than human-induced stressors (e.g. water pollution and hydromorphological alterations). More broadly, our results suggest that management needs to embrace the possibilities of gathering high spatial and taxonomical resolution data when analysing and predicting flow variation and climate change effects in order to preserve and restore functionally diverse communities. Moreover, to develop environmental flow schemes or restoration and climate change adaptation strategies for freshwater communities, local and regional processes need to be addressed simultaneously; equally responsible as drivers of community diversity.