Water temperature and river discharge are critical cues shaping biological processes of aquatic organisms. However, climate change can disrupt the duration and frequency of specific associations between water temperature and discharge, potentially hindering processes such as migration, reproduction or feeding. In this study over a large European basin, we compiled long-term upstream fish passage data for three diadromous fish species and time series of water temperature and current velocity reconstructed using physically-based thermal and hydrological models. We first identified days exhibiting high numbers of upstream fish passages and their corresponding water temperature-current velocity associations (defined as ”suitable days”). We then investigated trends in occurrence of suitable days for the upstream migration of diadromous fish over the period 1963-2019. Our results showed that the impacts of climate change on days with suitable associations appear to be species-specific. We found decreases in occurrence of suitable days for the upstream migration of Atlantic salmon mainly in the southern part of the basin for salmon migrating in spring and in the middle reaches scattered across the basin for fall salmon. On the other hand, days with suitable associations for upstream migration have predominantly increased for allis shad and sea lamprey across the whole basin. This study offers practical insights into how changing environmental conditions have affected the upstream migration of three diadromous species.