Climate change due to global warming is a public concern in Central Asia. Because of specific orography and climate conditions, the republic of Tajikistan is considered as the main glacial center of Central Asia. In this study, regional climate change impacts in the two large basins of Tajikistan, Pyanj and Vaksh River basins located in the upstream sector of the Amu Darya River basin are analysed. A statistical regression method with model output statistics corrections using the ground observation data, Willmott archived dataset and GSMaP satellite driven dataset, was developed and applied to the basins to downscale the Global Climate Model Projections at a 0.1-degree grid and to assess the regional climate change impacts at subbasin scale. It was found that snow and glacier melting are of fundamental importance for the state of the future water resources and flooding at the target basins since the air temperature had a clearly increasing trend toward the future. It was also found that the snowfall will decrease, but the rainfall will increase because of the gradual increase in the air temperature. Such changes may result in an increase in flash floods during the winter and the early spring, and in significant changes in the hydrological regime during a year in the future. Furthermore, the risks of floods in the target basins may be slightly increasing because of the increase in the frequencies and magnitudes of high daily precipitation and the increase in the rapid snowmelt with high air temperatures toward the future. Copyright © 2012 John Wiley & Sons, Ltd.