This paper presents estimates of water resources changes in three river basins in the Hindukush–Karakorum–Himalaya (HKH) region associated with climate change. The present climate (1961–1990) and future climate SRES A2 scenario (2071–2100) are simulated by the PRECIS Regional Climate Model at a spatial resolution of 25 × 25 km. Two HBV models (i.e. HBV-Met and HBV-PRECIS) are designed to quantify the future discharge. HBV-Met is calibrated and validated with inputs from observed meteorological data while HBV-PRECIS is calibrated and validated with inputs from PRECIS RCM simulations for the current climate. The future precipitation and temperature series are constructed through the delta change approach in HBV-Met, while in HBV-PRECIS future precipitation and temperature series from PRECIS RCM are directly used. The future discharge is simulated for three stages of glacier coverage: 100% glaciers, 50% glaciers and 0% glaciers. Generally temperature and precipitation shows an increase towards the end of 21st century. The efficiencies of HBV-Met during calibration and validation are higher compared to the HBV-PRECIS efficiencies. In a changed climate, discharge will generally increase in both models for 100% and 50% glacier scenarios. For the 0% glacier scenario, HBV-Met predicts a drastic decrease in water resources (up to 94%) in contrast to HBV-PRECIS which shows only a decrease up to 15%. Huge outliers in annual maximum discharge simulated through HBV-Met indicate that hydrological conditions are not predicted perfectly through the delta change downscaling approach. The results for HBV-Met simply confirm that the quality of observed data in this region is poor. The HBV-PRECIS model results are indicative of the higher risk of flood problems under climate change. The climate change signals in all three river basins are similar however, there are differences in the evaluated future water resources estimated through HBV-Met, whereas in HBV-PRECIS the changes in water resources are similar. This shows that the transfer of climate change signals into hydrological changes is more consistent in HBV-PRECIS than in HBV-Met. One of the reasons of the poorer results of the delta change approach is that in this approach the frequency of rainy days is not changed and day to day variability in temperature is not correctly transferred. However more research is needed to evaluate the uncertainties in both downscaling approaches. Moreover, the dynamical downscaling approach needs to be tested with other RCMs and preferably to other river basins as well.