Over the recent years, several research efforts investigated the impact of climate change on water resources for different regions of the world. The projection of future river flows is affected by different sources of uncertainty in the hydro-climatic modelling chain. One of the aims of the QBic3 project (Québec-Bavarian International Collaboration on Climate Change) is to assess the contribution to uncertainty of hydrological models by using an ensemble of hydrological models presenting a diversity of structural complexity (i.e., lumped, semi distributed and distributed models). The study investigates two humid, mid-latitude catchments with natural flow conditions; one located in Southern Québec (Canada) and one in Southern Bavaria (Germany). Daily flow is simulated with four different hydrological models, forced by outputs from regional climate models driven by global climate models over a reference (1971–2000) and a future (2041–2070) period. The results show that, for our hydrological model ensemble, the choice of model strongly affects the climate change response of selected hydrological indicators, especially those related to low flows. Indicators related to high flows seem less sensitive on the choice of the hydrological model.