Understanding temporal variability in water quality in the Three Gorges Reservoir (TGR) is crucial for evaluating environmental effects of damming and protecting China's largest freshwater resource. This study examined water quality changes in the main channel of the Yangtze River after dam completion as well as its relationship with water level fluctuation (WLF), controlled by annual impoundment operations and conditioned by flooding. Finally, the mass balance budget and integrative water quality indexing (WQI) methods were applied to elucidate the status of overall water quality since dam completion. Results showed that TGR outlet water (Yichang) exhibited higher pH and CODMn values and lower concentrations of dissolved oxygen (DO) and ammonia nitrogen (NH3-N) than inlet water (Zhutuo). Temporal variations in water quality parameters displayed similar trends for the outlet and inlet. Water quality parameters all showed negative correlations to water level, revealing the different effects of damming on water quality. It was estimated that reservoir impoundment led to a DO depletion of 1495.5 (+/- 1482.0) x 10(3) tons/yr and a CODMn increase of 564.0 (+/- 405.0) x 10(3) tons/yr, likely deriving from various internal pollutant loads from the WLF zone and tributary watersheds. According to WQI, TGR water quality remained at healthy levels. However, WQI linear regression showed that water quality at the outlet significantly decreased over time, indicating that the construction of the Three Gorges Dam generally caused water quality deterioration. Further investigation is required to determine the spatial distribution of point and non-point pollution sources and to identify major factors that influence TGR water quality.