Fish communities are characterized by a high degree of variability in space and in time, which mostly results from the influence of physical processes. Identifying the main variables governing changes in fish communities, as well as quantifying their influence, are basic in an attempt to assess anthropogenetic impacts. In south-eastern France, the Durance River is a Mediterranean, highly regulated river. The water resource is used to fulfill various human needs, including hydropower generation, drinkable water supply, or irrigation for agriculture. The hydroelectric scheme of the Durance River, decided in 1955, now numbers 19 electricity generation plants all along the river course. Human influences are therefore huge on the ecosystem, and include multiple and combined stressors. Here, we focused on the relationships between changes in fish assemblage structure and flow variables that depend on the hydropower plants functioning. Fish were sampled by electrofishing at 6 sites along the medium and lower Durance River. Sampling spanned the years 2005-2011, and was performed annually at the end of summer or early autumn. Multivariate analyses were performed to analyze the spatial-temporal pattern of fish assemblage variation across the 6 sites for 7 years, and to test whether inter-annual changes in seasonal flow characteristics could explain part of the taxonomic structure of fish assemblages. Analyses revealed a strong spatial structure along the 6 sites, with 31.5 % of total inertia being due to the site effect. Assemblages through time were alternatively dominated by subsets of species, whose relative dominance significantly depended on the flood magnitude. Toxonomic responses were relevant with expectations based on our biological and ecological knowledge of these species. Such a multiple site and year approach helped understanding the consequences of flow regulation on biological assemblages in a large river, and allowed flow management guidelines to be suggested.