Water scarcity is influencing environmental and socio-economic development on a global scale. Pakistan is ranked third among the countries facing water scarcity. This situation is currently generating intra-provincial water disputes and could lead to transboundary water conflicts. This study assessed the future water resources of Astore basin under representative concentration pathways (RCP) 4.5 and 8.5 scenarios using fully distributed TOPographic Kinematic APproximation and Integration (TOPKAPI) model. TOPKAPI model was calibrated and validated over five years from 1999–2003 with a Nash coefficient ranging from 0.93–0.97. Towards the end of the 21st century, the air temperature of Astore will increase by 3°C and 9.6 °C under the RCP4.5 and 8.5 scenarios, respectively. The rise in air temperature can decrease the snow cover with Mann Kendall trend of –0.12%/yr and –0.39%/yr (p ≥ 0.05) while annual discharge projected to be increased 11% (p ≤ 0.05) and 37% (p ≥ 0.05) under RCP4.5 and RCP8.5, respectively. Moreover, the Astore basin showed a different pattern of seasonal shifts, as surface runoff in summer monsoon season declined further due to a reduction in precipitation. In the spring season, the earlier onset of snow and glacier melting increased the runoff due to high temperature, regardless of the decreasing trend of precipitation. This increased surface runoff from snow/glacier melt of Upper Indus Basin (UIB) can potentially be utilized to develop water policy and planning new water harvesting and storage structures, to reduce the risk of flooding.