Water resources are essential to ecosystems and social economies worldwide, especially in the deserts and oases of the Tarim River Basin, whose water originates largely from alpine mountains characterized by complicated hydrological processes and scarce hydrometeorological observations. This paper presents multisite and multiobjective modeling of hydrological processes in the whole Tarim River Basin, covering 32 catchments in total. The study uses the Soil and Water Assessment Tool, extended by incorporating a degree‐day glacier melt module to enable modeling of glacier melt in the alpine mountains. The multiobjective calibration approach of ε‐Nondominated Sorting Genetic Algorithm‐II was implemented with the two objective functions of the Nash‐Sutcliffe value of daily streamflow and the bias of simulated glacier melt contribution to streamflow. Based on the combined use of the Morris sensitivity technique and hierarchy cluster, the 32 catchments in the study area are divided into six groups according to their dominating hydrological processes, for example, glacier melt, snowmelt, groundwater, and routing. The multiobjective calibration was satisfactory, with 22 of the 32 catchments showing Nash‐Sutcliffe values of daily streamflow larger than 0.6 and the bias of simulated glacier melt contribution to streamflow values smaller than 0.05. Model performance was highly dependent on meteorological data availability, in that low data availability led to poor model performance, while factors such as catchment area and mean annual snowfall had little influence on model performance. The results indicate that multisite and multiobjective calibration enables consistent and comprehensive examination of the spatially different hydrological processes in a large basin and provides information for further assessment of the impact of climate change on water availability.