Understanding how climate change would affect biota inhabiting sensitive and highly valuable ecosystems, spanning broad regions, is essential to anticipate implications for biodiversity and humans, and to identify management and mitigation measures. Traditionally, assessments to evaluate climatic risks over broad regions and for many species implement models that allow the projection of a climate-driven redistribution of biodiversity. Still, the wealth and quality of the background information (e.g., species presence data) constrain the accuracy and representativeness of such frameworks. As an alternative, here, we developed a twofold approach to assess the vulnerability of 86 European freshwater fish. We accounted for shifts in a multidimensional climatic space of broader hydrological units that host freshwater bodies in Europe. We then linked metrics of their climatic stability with groups of species, which were generated from six intrinsic traits that shape species adaptive capacity to climate change. Our results demonstrated that the climate of all (n = 538) river sub-basins hosted in the European Union territory would change by 2100, with more than 10% of them being projected to gain completely novel climates. Sub-basins predicted to lose more than 90% of their current climatic space were mainly identified in the area around the Baltic Sea, but also in Mediterranean regions (i.e., Iberian Peninsula). Important numbers of fish species with life history strategies that are considered susceptible to climate change were identified in sub-basins that were predicted to completely lose their current climatic conditions. Clearly, the climate of valuable freshwater ecosystems is changing, affecting species and their communities in varying ways. The risk is high, and is not limited to specific regions; thus, new effective strategies and measures are needed to conserve freshwater fish and their habitats across Europe.