Increased flood risks have been projected, but with large uncertainties, in the Kabul River Basin (Afghanistan and Pakistan). To place future changes in a long-term perspective, we produce a 382-year precipitation reconstruction for the basin using seven tree-ring chronologies of old-growth conifers from the Hindu Kush Mountains, a monsoon-shadow area. The reconstruction proves robust over rigorous cross-validations (R2 = 0.60, RE = 0.60, CE = 0.53). The full reconstruction (1637–2018) reveals a steady decline in the low end of the precipitation distribution, implying increasing drought risks. We show that droughts are getting more severe, shorter, and more frequent, interspersed with more frequent pluvials in the past century. Drought risks, compounded with projected flood intensification, pose significant threats for this transboundary river. Therefore, future water management needs to account for both flood and drought risks and be informed by long-term hydroclimatic variability.