Most key life-cycle events of organisms are synchronized by complex interactions of environmental cues to ensure optimal survival and growth of individuals and their offspring. However, this synchronicity is threatened by global change, which modifies the hydrological and thermal regimes of rivers worldwide. In particular, the asynchronous evolution of river temperature and flow can alter the duration and frequency of environmental windows suitable for the migration of diadromous fish. In this research project, we first developed the ‘Choc’ method to explore temporal CHanges in the OCcurrence of associations in bivariate time series. We applied this method to several case studies, which highlighted how global change has altered the conditions under which the endangered European eel and Atlantic salmon migrate, and how they have responded to these environmental changes. Recently, reconstructed (1963-2019) and projected (2020-2100) daily river temperature and flow data have been modelled over the entire hydrographic network of the Loire catchment (France). We combined this extensive dataset with daily fish passages available at fishways to assess the spatial and seasonal variability of trends in temperature-flow associations at a large scale. We then described how it has affected and will likely affect migration conditions of Atlantic salmon, allis shad and sea lamprey in the Loire catchment. Finally, we developed indicators to quantify past, present and future environmental suitability for their migration that allow comparison between rivers and tributaries, thereby providing operational results for the conservation of diadromous species and the prioritization of management actions in the context of global change.