Recent researches on the Yangtze River and the Jialing River water in Chongqing section of the Three Gorges Reservoir indicate that the pH value is relatively high and the CODMnconcentration is more than 4.5 mg/L in most of the time. Especially the proportion of dissolved molecule organic is high, as well as the high turbidity during the summer flood period. And the organic contamination is relatively serious. The fuzzy weighted water quality coefficient and hierarchical cluster analysis methods are applied to evaluate and sort the characteristic qualities of two-river water sources. During the research period, the results show that the Yangtze River water source quality is characterized by high turbidity and polluted of summer stage, middle temperature and micro-polluted of spring-autumn stage and low temperature and micro-polluted of winter stage. The Jialing River water source quality is characterized by low turbidity stage, high alga-polluted of early spring stage and high temperature and polluted of winter stage. Due to the various water qualities of two-river water sources at different periods, it is hard to meet the requirement of Standards for Drinking Water Quality (GB 5749-2006) by using traditional water treatment technologies. So the research on enhanced treatment is necessary.