Investigation of water sources and flow pathways is crucial to understand and evaluate the characteristics of surface water and groundwater systems. This article aims to identify the hydrochemical and hydrological processes in different landscape zones based on hydrochemical analyses of various samples, including samples from glacier, snow, frozen soil meltwater, surface water, groundwater, and precipitation, in the alpine cold region of China. Hydrochemical tracers indicated that chemical compositions are characterized by the Ca-HCO₃ type in the glacier-snow zone; the Mg-Ca-SO₄ type in the alpine cold desert zone; the Ca-HCO₃-SO₄ type in the marsh meadow zone; the Ca-Mg-HCO₃ type in the alpine shrub zone; and the Ca-Na-SO₄ type in the mountain grassland zone. An end-member mixing model was used for hydrograph separation. The results showed that the Mafengou River in the wet season was recharged by groundwater in the alpine cold desert and alpine shrub zones (67%), surface runoff in the glacier-snow zone (11%), surface runoff in the alpine cold desert zone (8%), thawed water from frozen soil in the marsh meadow and mountain grassland zones (9%), and direct precipitation on the river channel (5%). This study suggests that precipitation from the whole catchment yielded little direct surface runoff; precipitation was mostly transformed into groundwater or interflow and was then concentrated into the river channel. This study provides a scientific basis for evaluation and management of water resources in the basin.