Future hydrological extremes, such as floods and droughts, may pose serious threats for the livelihoods in the upstream domains of the Indus, Ganges, Brahmaputra. For this reason, the impacts of climate change on future hydrological extremes is investigated in these river basins. We use a fully-distributed cryospheric-hydrological model to simulate current and future hydrological fluxes and force the model with an ensemble of 8 downscaled General Circulation Models (GCMs) that are selected from the RCP4.5 and RCP8.5 scenarios. The model is calibrated on observed daily discharge and geodetic mass balances. The climate forcing and the outputs of the hydrological model are used to evaluate future changes in climatic extremes, and hydrological extremes by focusing on high and low flows. The outcomes show an increase in the magnitude of climatic means and extremes towards the end of the 21st century where climatic extremes tend to increase stronger than climatic means. Future mean discharge and high flow conditions will very likely increase. These increases might mainly be the result of increasing precipitation extremes. To some extent temperature extremes might also contribute to increasing discharge extremes, although this is highly dependent on magnitude of change in temperature extremes. Low flow conditions may occur less frequently, although the uncertainties in low flow projections can be high. The results of this study may contribute to improved understanding on the implications of climate change for the occurrence of future hydrological extremes in the Hindu Kush–Himalayan region.