Alteration of natural river flow regimes is a major threat to freshwater biodiversity. Restoration of natural flow regimes requires an understanding of linked hydrological and ecological processes. In this study, we investigated how annual seasonal flow characteristics and physical habitat attributes could interact to explain yearly changes in brown trout population densities (for 0+ fish, corresponding to the young of the year, and for the >0+ age class) in 112 sites widespread in France. Using an information theoretic approach and general linear modeling, we identified the physical habitat attributes and seasonal hydrological variables which explained 0+ proportion, total, >0+ and 0+ brown trout density dynamics. A decrease in total and 0+ brown trout densities were mainly linked to high water levels in both high and low flows during the emergence period and to a lesser extent, to physical habitat attributes reflecting the river size. 0+ proportions were only linked to the level of low flows, and to a lesser extent to high flows, during the emergence period. Our study demonstrated that seasonality of flow is a main driver of brown trout population dynamics, especially magnitude of high and low flows for the 0+ age class, and should be considered in the definition of environmental flows.