Himalayan high-altitude catchments are crucial sources of freshwater, supporting essential activities both upstream and downstream. However, the warming climate is causing the cryospheric cover to diminish, affecting freshwater availability throughout the Himalayan catchments. Therefore, understanding the hydrological processes shaping the regional water cycle is vital for effective water resource management policies. The dataset reveals significant spatial and temporal variability in meltwater without clear isotopic signatures of different river flow sources. Nevertheless, distinctive signatures of river/stream flow sources emerge at the sub-basin or catchment scale due to changing physiographical, meteorological, and local climatic conditions. Microclimatic factors like altitude variation and aspect slope further influence the spatio-temporal variability in water sources and streamflow, resulting in different lapse rates at the sub-basin/catchment level. This study highlights that the contribution of snowmelt and glacier melt to river flow varies across space and time, with snowmelt dominating in the Indus while glacier melt dominates in the Suru catchment. The rugged topography and microclimate of the Upper Indus River Basin (UIRB) primarily govern the diverse contributions from various river flow sources. With a warming climate leading to reduced solid precipitation, continuous glacier mass loss, and early snow cover melting, the perennial flow of rivers is expected to be impacted inconsistently. This has the potential to disrupt the economic and political stability of the region.