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Studies on hydrological processes are often emphasized in resource and environmental studies. This paper identifies the hydrological processes in different landscape zones during the wet season based on the isotopic and hydrochemical analysis of glacier, snow, frozen soil, groundwater and other water sources in the headwater catchment of alpine cold regions. Hydrochemical tracers indicated that the chemical compositions of the water are typically characterized by: (1) Ca?HCO3 type in glacier snow zone, (2) Mg?Ca?SO4 type for surface runoff and Ca?Mg?HCO3 type for groundwater in alpine desert zone, (3) Ca?Mg?SO4 type for surface water and Ca?Mg?HCO3 type for groundwater in alpine shrub zone, and (4) Ca?Na?SO4 type in surface runoff in the alpine grassland zone. The End-Members Mixing Analysis (EMMA) was employed for hydrograph separation. The results showed that the Mafengou River in the wet season was mainly recharged by groundwater in alpine cold desert zones and shrub zones (52%), which came from the infiltration and transformation of precipitation, thawed frozen soil water and glacier-snow meltwater. Surface runoff in the glacier-snow zone accounted for 11%, surface runoff in alpine cold desert zones and alpine shrub meadow zones accounted for 20%, thawed frozen soil water in alpine grassland zones accounted for 9% of recharge and precipitation directly into the river channel (8%). This study suggested that the whole catchment precipitation did not produce significant surface runoff directly, but mostly transformed into groundwater or interflow, and finally arrived in the river channel. Copyright (c) 2011 John Wiley & Sons, Ltd.