Abstract: The alpine region serves as an important water source for downstream areas, and its runoff processes are highly complex due to the influence of underlying surface conditions such as permafrost. Compared to large-scale watersheds, small watersheds are more suitable for elucidating the dominant role of the underlying surface in hydrological processes, However, related research remains limited due to data scarcity caused by harsh environmental conditions in high-altitude areas. To further elucidate the spatiotemporal variations in river runoff sources at the small-watershed scale, this study takes the Hulu watershed in the upper reaches of the Heihe River as an example. By integrating water-stable isotopes with hydrometeorological observations, the MixSIAR model was applied to quantitatively determine the runoff components in the periglacial bedrock area, permafrost area, and seasonally frozen-ground area. The results show that in March, runoff in the seasonally frozen-ground area was dominated by baseflow (98%), while other regions experienced flow cessation. In May, glacier-snow meltwater and snowmelt were the main sources in both the periglacial bedrock area and permafrost area, although baseflow remained dominant in the seasonally frozen-ground (62%). From July to September, glacier-snow meltwater became the primary source in the periglacial bedrock and permafrost areas, whereas baseflow continued to dominate in the seasonally frozen-ground area (more than 63%). The findings indicate that meteorological factors are the primary drivers of runoff variation, while underlying surface conditions—such as permafrost distribution and aquifer characteristics—play a critical regulatory role in water-source composition. This study enhances the understanding of hydrological processes in small alpine regions and provides theoretical support for water resource management in cold environments.