The Mediterranean region is a climate change hotspot for water resources. However, uncertainty analyses of hydrological projections are rarely quantified. In this study, an in-depth analysis of projections and uncertainties for high and low flows is performed. Climatic projections derived from a recent downscaling method were used, for two representative concentration pathway scenarios (RCPs), five general circulation model/regional climate model (GCM/RCM) couples, three hydrological models (HMs), and 29 calibration schemes. A quasi-ergodic analysis of variance was used to evaluate the contribution of each impact modelling step to the total uncertainty. For high flows, the results show a mean increase of 30% by 2085, and RCPs make the highest contribution to the total uncertainty, followed by GCMs. For low flows, 50% of projections indicate a decrease of 7% or more by 2085, and HM structures, hydrological model parameters, and GCMs are the most important uncertainty sources. These results contribute to raise awareness among water managers regarding future hydrological extreme events.