Increased flood risks have been projected in the Kabul River Basin, but with large uncertainties. To place future changes in a long-term perspective, we produce a 501-year precipitation reconstruction for the basin using seven tree-ring chronologies of Cedrus deodara, Picea smithiana, and Pinus gerardiana from the Hindukush Mountains, a monsoon-shadow area. The reconstruction proves robust over rigorous cross-validations (R2 = 0.62, RE = 0.61, CE = 0.53). The full reconstruction (1517–2018) shows heterogeneous changes in the precipitation distribution: there is a weak increasing trend in the median annual precipitation, no apparent trend in the 50-year maximum precipitation, and, importantly, a steadily decreasing trend in 50-year minimum precipitation. In other words, our reconstruction shows that drought risks have been increasing over the past five centuries. Drought risks, compounded with projected flood intensification, pose significant threats for the transboundary river. Future water management decisions should factor in past long-term climate variability.