Spatial Process in Hydrology (SPHY) is a hydrological modeling tool, which is a structured spatially distributed model with characteristics allied with a “leaky bucket,” and it operates at 250–500 m resolution. The model utilizes various high-resolution thematic maps as inputs to estimate the snow and glacier melt runoff separately. In this study, SPHY was employed to assess the runoff of the Trishuli basin, located in central Nepal. Trishuli basin is one of the major tributaries of the Narayani river basin, stretching from the northern border with Tibet to the southern reaches to the Siwalik Hills. The model has been integrated with variable degree-day factors along with a temperature index model. The SPHY-simulated total runoff at two different stations (Betrawati and Kyanjin) in the Trishuli basin were estimated for HY 2006–2007 and HY 2020–2021. The calculated annual average runoff at Betrawati shows a decline in glacier melt runoff by 45 times and in Kyanjin, it was observed to be decreased by 5 times in a span of 15 years. The study emphasizes the hydrological dynamics of the Trishuli basin and points out the significance of snow and glacier melt runoff that are influenced by climate conditions.