Aim - Rivers belong to the most threatened ecosystems on Earth. Historical anthropogenic alterations have, and future climate change will further affect rivers and the species therein. While many studies have projected climate change effects on species, little is known about the severity of these changes compared to historical alterations. Here, we used a unique 300-year time series of hydrological and climate data to explore the vulnerability of 48 native fish species in the upper Danube River Basin to past and potential future environmental changes. Location - Upper Danube River Basins (Germany and Austria). Methods - We applied a climate niche factor analysis and calculated species-specific vulnerability estimates based on modelled and observed hydrological and climate data from 1800 to 2100. We compared the estimated species vulnerabilities between two historical time intervals (1800–1830 and 1900–1930) and a future time interval (2070–2100, including the two representative concentration pathways 4.5 and 8.5) to an observed reference time interval (1970–2000). In addition, we identified the main environmental drivers of species vulnerability and their change over the past 200 years and for the predicted 100 years in the future. Results - Our results showed that (i) in the past, species vulnerability was mainly driven by changes in discharge, while (ii) future potential vulnerabilities would be due to temperature. Moreover, we found that (iii) future environmental conditions for riverine fish species driven by temperature would change at a similar magnitude as past hydrological changes, driven by anthropogenic river alterations. Future changes, projected for the RCP 4.5, would result in moderate species vulnerability, whereas for the RCP 8.5, the vulnerability for all species would substantially increase compared to the historical conditions. Main Conclusion - Accounting for an extended timeline uncovers the extent of historical pressures and provides unprecedented opportunities to proactively plan conservation strategies that are necessary to address future challenges.