In order to explore the hydrochemical characteristics, influencing factors, and water quality of various water bodies in Bangong Co Lake Watershed, 60 water samples were collected from lake, river, groundwater, glacier water bodies in the watershed. Piper diagram, Gibbs’ diagrams, ion ratio analysis, statistical methods, and principal component analysis were used to study the hydrochemical characteristics and its influencing factors. Drinking water quality index (DWQI) and USSL classification were applied to assess the groundwater quality suitability for agricultural and drinking purposes. The hydrochemical characteristics show the differences among water bodies and their spatial distribution. Analyzed groundwater and surface water samples such as river water and glaciers mainly presented Ca-HCO3 type, and lake water mainly presented Na-Cl type and a small number of Na-HCO3·Cl type. The lake water chemical components are mainly affected by evaporative karst decomposition. The main mineralization process of groundwater and river water was related to the dissolution of reservoir minerals such as dolomite and calcite, and halite. The DWQI indicates that 79% of the groundwater samples in the study area showed a good quality for drinking. For irrigation water quality, the electrical conductivity (EC), calculated Sodium adsorption ratio (SAR), Magnesium hazardous ratio (MHR) showed that more than 13% of the total samples were not suitable for irrigation. USSL classification indicated that glacier and river water are relatively suitable for irrigation. And part of the groundwater and lake water has very high alkalinity or salinity which is alarming when considered for irrigation.