Due to anthropogenic actions, species have become endangered or have been driven to the verge of extinction, requiring conservation plans to be developed and implemented. These plans include measures to protect and enhance remaining populations and to reintroduce populations within the native ranges. However, future habitat suitability in the face of climate change is rarely assessed, despite the fact that it could compromise conservation opportunities. It is attempted to carry this task out for the critically endangered European Atlantic sturgeon (Acipenser sturio). Species presence/absence was documented for 196 basins between 1750 and 1850 over the Western Palearctic. A predictive distribution model was established from this database using Boosted Regression Trees (BRT) and a pool of relevant environmental variables. Projections were performed at two time-steps, 2050 and 2100, using the HadCM3 Global Climate Model (GCM) and the A2 and A1FI emissions scenarios. The BRT model incorporated two general climatic descriptors, summer precipitation and annual air temperature, average slope served as a topographic predictor, and marine provinces as a macroecological variable. The statistical model performance allowed projections with the predictive deviance being 29 ± 2.80 and the Area Under the Curve (AUC) being 0.86 ± 0.02. The results obtained are in accordance with the species thermal preferences and with its hydrological habitat requirements. Most of the former sturgeon distribution range was assessed as being strongly affected by climate change, especially basins along the southern limit of its range. On this basis, proposals to integrate the climate change dimension into conservation strategy are discussed.