Stream temperature and discharge are two fundamental triggers of key periods of the life cycle of aquatic organisms such as the migration of diadromous fish. However, the increase in stream temperature, more frequent and severe droughts, and asynchronous evolution of stream temperature and discharge due to climate change can modify the duration and frequency of favorable temperature-flow associations for the realization of species’ ecological processes. In this study, we investigated the influence of changes in favorable temperature-flow velocity associations for the upstream migration of Atlantic salmon, Alis shad and Sea lamprey at the scale of the Loire River basin (100000 km²). First, we used a physically-based thermal model (T-NET), coupled with a semi-distributed hydrological model (EROS) to reconstruct continuous daily times series over the 1963-2019 period (Seyedhashemi et al., 2022). Current velocity (V) was estimated using discharge through a hydraulic geometry model (Morel et al., 2020). We identified suitable water temperature-flow velocity associations for the migration of the three studied species based on (1) the literature and (2) observed migration recorded at fish passage stations. Using the “Choc method” (Arevalo et al., 2020), we then quantified the changes in frequency of occurrence of these suitable environmental windows over the past six decades across the hydrographic network of the Loire River basin. Our results showed that the greatest increases in stream temperature were associated with the greatest decreases in flow velocity over the past six decades. We also found that the frequency of suitable temperature-velocity associations for upstream migration of Atlantic salmon has significantly reduced, mainly in the southern part of the basin. In contrary, the frequency of suitable associations for upstream migration of the two other species has mainly increased. These results highlighted strong disparities in the consequence of global changes on fish migratory processes among species and in space. This work provides operational results for the management of these threatened diadromous species and the prioritization of management measures in a context of climate change.