The integrated use of isotopic and hydrochemical tracers is an effective way to investigate hydrological processes on a range of spatial and temporal scales. This study investigated stable isotopes and hydrochemistry of the river water in the Qinghai Lake Basin, and discussed relationships between runoff and variations of air temperature and precipitation. Results indicated that all of the river water points lie close to the local meteoric water line (LMWL); and the slope of local evaporation line of river water samples (6.82) was smaller than that of the LMWL (7.98), indicating that the river water mainly originated from the precipitation in the catchments which underwent weak evaporation. The river water in the tributaries would undergo relatively stronger evaporation than that in the main stream. The hydrochemical type of river water was Ca-Mg-HCO3, and the river water chemistry was mainly controlled by carbonate dissolution in the Qinghai Lake Basin. The river discharge was generated mainly from the middle and upper catchment. The runoff depths of Buha River Catchment and Shaliu River Catchment were 91.0 mm and 283.4 mm, respectively; and the runoff coefficients were 0.164 and 0.531, respectively. Because of a relatively longer channel, larger drainage area and smaller gradient, the surface water flowed more slowly and infiltrated more in the large river catchment; therefore, the runoff coefficient in the large river catchment was smaller than that in the relatively smaller catchment. The river runoff in the Qinghai Lake Basin was primarily influenced by precipitation. This study provides insights into the hydrological and geochemical processes of cold and alpine rivers, along with water resource management options in the Qinghai Lake Basin and northeast Qinghai-Tibet Plateau.