There is growing evidence that climate change will alter water availability in Europe. Here, we investigate how hydrological low flows are affected under different levels of future global warming (i.e., 1.5, 2 and 3 K). The analysis is based on a multi-model ensemble of 45 hydrological simulations based on three RCPs (rcp2p6, rcp6p0, rcp8p5), five CMIP5 GCMs (GFDL-ESM2M, HadGEM2-ES, IPSL-CM5A-LR, MIROC-ESM-CHEM, NorESM1-M) and three state-of-the-art hydrological models (HMs: mHM, Noah-MP, and PCR-GLOBWB). High resolution model results are available at the unprecedented spatial resolution of 5 km across the pan-European domain at daily temporal resolution. Low river flow is described as the percentile of daily streamflow that is exceeded 90 % of the time. It is determined separately for each GCM/HM combinations and the warming scenarios. The results show that the change signal amplifies with increasing warming levels. Low flows decrease in the Mediterranean while they increase in the Alpine and Northern regions. In the Mediterranean, the level of warming amplifies the signal from −12 % under 1.5 K to −35 % under 3 K global warming largely due to the projected decreases in annual precipitation. In contrast, the signal is amplified from +22 % (1.5 K) to +45 % (3 K) in the Alpine region because of the reduced snow melt contribution. The changes in low flows are significant for regions with relatively large change signals and under higher levels of warming. Nevertheless, it is not possible to distinguish climate induced differences in low flows between 1.5 and 2 K warming because of the large variability inherent in the multi-model ensemble. The contribution by the GCMs to the uncertainty in the model results is generally higher than the one by the HMs. However, the uncertainty due to HMs cannot be neglected. In the Alpine and Northern region as well as the Mediterranean, the uncertainty contribution by the HMs is partly higher than those by the GCMs due to different representations of processes such as snow, soil moisture and evapotranspiration.