Climate-driven changes in glacier-fed streamflow regimes have direct implications on freshwater supply, irrigation and hydropower potential. Reliable information about current and future glaciation and runoff is crucial for water allocation, a complex task in Central Asia, where the collapse of the Soviet Union has transformed previously interdependent republics into autonomous upstream and downstream countries. Although the impacts of climate change on glaciation and runoff have been addressed in previous work undertaken in the Tien Shan (known as the ‘water tower of Central Asia’), a coherent, regional perspective of these findings has not been presented until now. Here we show that glacier shrinkage is most pronounced in peripheral, lower-elevation ranges near the densely populated forelands, where summers are dry and where snow and glacial meltwater is essential for water availability. Shifts of seasonal runoff maxima have already been observed in some rivers, and it is suggested that summer runoff will further decrease in these rivers if precipitation and discharge from thawing permafrost bodies do not compensate sufficiently for water shortfalls.