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China’s “Environmental Quality Standards for Surface Water” (GB3838-2002) was combined with the Canadian Council of Ministers of the Environment Water Quality Index (CCME-WQI) to evaluate the water quality of the Three Gorges Reservoir (TGR) of China. The CCME-WQI values indicated that the overall water quality in the TGR remained stable and was ranked as “good” during the period 2010–2013. The water quality at the inflow sections of the Jialing and Wu Rivers was worse than that of the main channel (the Yangtze River), especially for backwater sections of these two tributaries. Total nitrogen, total phosphorus, and fecal coliform amounts were the three key pollutants affecting the water quality of the TGR. During low-water-level operation periods, the water quality of the TGR deteriorated. Human activities, such as the seasonal fertilization of croplands, appeared to be the main cause of the variation in water quality in different operation cycles. However, the relationship between water quality and reservoir operation cycles is complex and requires more research and data to be clarified. The CCME-WQI can be used to easily qualitatively and quantitatively assess whether the overall water quality meets the specified water objectives, and provides a clear indication of the water category. Compared with the single factor pollution index (SFPI) method, the CCME-WQI uses a group of typical criteria rather than worst-case criteria. The CCME-WQI, therefore, provides a more meaningful and comprehensive assessment than the SFPI method.