The Tien Shan and Pamir mountains host over 28,000 glaciers, providing essential water resources for increasing water demand in Central Asia. A disequilibrium between glaciers and climate affects meltwater release to Central Asian rivers, challenging the region's water availability. Previous research has neglected temporal variability. We present glacier mass balance estimates based on transient snowline and geodetic surveys with unprecedented spatio-temporal resolution from 1999/00–2017/18. Our results reveal spatio-temporal heterogeneity characterised by two mass balance clusters: (i) positive, low variability, and (ii) negative, high variability. This translates into variable glacial meltwater release ( ≈ 1% to 16%) of annual river runoff for two watersheds. Our study reveals more complex climate forcing-runoff responses and importance of glacial meltwater variability for the region than suggested previously.