As a vital indicator of watershed ecosystem, water quality has essential implications for the development of the ecological environment and economic society. Meanwhile, water quality assessment provides indispensable support for the integrated control of water pollution. The water quality of surface waters (i.e. lake and river waters) and drinking waters (i.e. well and tap waters) has been investigated in Yamzhog Yumco Basin since 2010 and 2012, respectively. Based on the annual average data, the pollution factors of waters in Yamzhog Yumco Basin were analyzed by utilizing the single factor pollution evaluation method, and the present situation of water quality exerted as well with the Nemerow pollution index method. The analysis revealed that the Yamzhog Yum Co and the Bajiu Co are both moderately polluted, while the other 10 surface waters are clean or almost clean. Moreover, the selenium and fluoride contents are generally exceeded or close to the upper limit of the standard range. Two thirds of the nine drinking waters are polluted to different degrees with the selenium, aluminum, and nitrate as the main pollution factors. In addition, the quality of tap waters is much better than that of well waters. Water pollutants, through the water-soil-plant-animal system, could cause the destruction of ecological environment, hinder the sustainable development of agriculture, and finally threaten human's health. Therefore, in order to control and reduce the water pollution in Yamzhog Yumco Basin, it is necessary to renovate the basin environment comprehensively, control the agricultural non-point pollution, and improve the drinking water facilities. Meanwhile, further water quality monitoring is valuable in such process.