The Himalayan mountain range produces one of the steepest and largest rainfall gradients on Earth, with >3 m/yr rainfall difference over a ∼100 km distance. The Indian Summer Monsoon (ISM) contributes more than 80% to the annual precipitation budget of the central Himalayas. The remaining 20% falls mainly during pre-ISM season. Understanding the seasonal cycle and the transfer pathways of moisture from precipitation to the rivers is crucial for constraining water availability in a warming climate. However, the partitioning of moisture into the different storage systems such as snow, glacier, and groundwater and their relative contribution to river discharge throughout the year remains under-constrained. Here, we present novel field data from the Kali Gandaki, a trans-Himalayan river, and use 4-year time series of river and rain water stable isotope composition (δ18O and δ2H values) as well as river discharge, satellite Global Precipitation Measurement amounts, and moisture source trajectories to constrain hydrological variability. We find that rainfall before the onset of the ISM is isotopically distinct and that ISM rain and groundwater have similar isotopic values. Our study lays the groundwork for using isotopic measurements to track changes in precipitation sources during the pre-ISM to ISM transition in this key region of orographic precipitation. Specifically, we highlight the role of pre-ISM precipitation, derived from the Gangetic plain, to define the seasonal river isotopic variability across the central Himalayas. Lastly, isotopic values across the catchment document the importance of a large well-mixed groundwater reservoir supplying river discharge, especially during the non-ISM season.