The spatiotemporal variations in stable isotope ratios are primarily related to atmospheric moisture transport. However, the isotopic composition of stream water is significantly influenced by the diverse landscape of glaciated and snow-dominated basins. The present study investigates the spatiotemporal variation of the isotopic composition of stream water and potential water sources such as rain, snowmelt, glacier melt, lakes, and groundwater in the Upper Jhelum River Basin (UJRB). Our findings reveal that the significant seasonal variability of precipitation is mainly associated with the transition between westerlies (WDs) and the Indian Southwest Monsoon (ISWM), each conveying distinct moisture to the UJRB. The isotopic signature in rain is actively controlled by the combined effect of temperature (T) and relative humidity (RH) during WDs. However, the impact of “amount effect” with lower condensation temperature is dominant during the latter half of ISWM. Seasonal variations in δ18O and d-excess in stream water are distinct, influenced by different contributing sources and topographic controls. A linear relationship is observed between δ18O vs. altitude and glacier area ratio (GAR). Lower δ18O in stream water and higher d-excess values are observed in the southwest at higher elevations in glacier-fed tributaries. On the northern side, higher δ18O in stream water indicates contributions from non-glacier fed tributaries and enhanced groundwater contributions rather than merely following the lower δ18O of precipitation along the strengthened WDs gradient. The δ18O isotopic lapse rate (ILR) of rain (−0.19‰/100 m) is higher compared to ILR for the river (−0.05‰/100 m), reflecting the mixing of water sources in river water. However, both are lower than the global average (−0.28‰/100 m). This study helps in understanding the influence of meteorological, topographic factors, and other water sources on stream water, a prerequisite for projecting a potential future change in the complex Himalayan region.