Projected snow cover and river flows are important for planning and managing water resources in snow-dominated basins of the Himalayas. To quantify the impacts of climate change in the data scarce Panjshir River basin of Afghanistan, this study simulated present and future snow cover area (SCA) distributions with the snow model (SM), and river flows with the snowmelt runoff model (SRM). The SRM used the degree-day factor and precipitation gradient optimized by the SM to simulate river flows. Temperature and precipitation data from eight kinds of general circulation models (GCMs) were used for bias correction. The SM and SRM were first calibrated and validated using 2009–2015 data, and then bias-corrected future climate data were input to the models to simulate future SCA and river flows. Under both the representative concentration pathways (RCP) 4.5 and 8.5, the annual average SCA and river flow were projected to decrease in the mid and late 21st century, although seasonal increases were simulated in some instances. Uncertainty ranges in projected SCA and river flow under RCP 8.5 were small in the mid 21st century and large in the late 21st century. Therefore, climate change is projected to alter high-altitude stream sources in the Hindukush mountains and reduce the amount of water reaching downstream areas. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.