Description: The Three Gorges Reservoir (TGR) has brought great socio-economic benefits and has had huge effects on the aquatic environment. The large scale and diversity of the TGR result in the variations of the water quality among the mainstream and its tributaries. Comprehensive understanding of the water quality status is crucial for water management and regional development of the TGR. Monthly data of 8 water quality parameters, including potential of hydrogen, biochemical indexes and nutrients indexes, were collected from 14 sampling sites distributed in the Yangtze River and four tributaries. The temporal and spatial distributions of each water quality parameter were presented, and the underlying causes were disclosed. The cluster analysis (CA) and the Canadian Council of Ministers of the Environment Water Quality Index (CCME-WQI) were adopted to analyze and assess the water quality statuses and trend. The results showed that most of the water quality parameters presented significant seasonal patterns due to the seasonality of hydrologic/hydraulic variables. Water quality status and pollution type varied among the mainstream and its tributaries, due to the spatial heterogeneity of geology, geomorphology and anthropogenic activities. NO 3 -N, TN and TP were identified as the key pollution indexes, presenting the enriched nutrients in the water body. A large proportion of NO 3 -N in the TN (over 80%) was linked to the abuse of chemical fertilizers. The water quality in the TGR cannot always reach natural or desirable levels at several of the sampling sites where development and urbanization are relatively high, such as those near the main urban area of Chongqing or the inflow section of the Wu River. This study is expected to have major implications for water quality analysis and assessment approaches and water environment protection and management at large scales.