We evaluated 4-year data set to assess the trophic state and limiting factors of the Three Gorges Reservoir (TGR) during the experimental impounding period (September 2005 to September 2007) and the normal operating period (September 2008 to September 2010). The results indicated that there had been appeared new characteristics in spatial and temporal distribution of trophic state indices after impoundment. The trophic state indices (TSI(TP)) showed increased trend after the TGR impoundment during the study area, but TSI(TN) and TSI(SD) had no significant changes after the TGR impoundment. The values of TSI(CHL) showed increased trend after the TGR impoundment in S1, and the values of TSI(CHL) did not show obvious changes in S2, S3 and S4 after the TGR impoundment. The values of TSI(TN), TSI(TP) and TSI(SD) show similar spatial variances with the highest value in S4, followed in a descending order by S3, S2 and S1. TSI(CHL) in the S2 and S3 were higher than that in S1 and S4. According to the characteristics of water level, the operational period of the TGR classified into following four stages: stage I (pre-November-April), stage II (May-July), stage III (July-September) and stage IV (September-November). The values of TSI(TN) and TSI(TP) in the Daning River and the TGR mainstream showed similar seasonal variances with the highest value in the stage II and III, followed in a descending order by stage I and IV. The values of TSI(CHL) varied substantially among the four stages, with the highest value in stage III, followed by stage II, IV and I. The trophic state indices differences were getting smaller between the four stages after the TGR impoundment. Using Carlson's two-dimensional approach, deviations of the TSI(S) indicated that factors other than phosphorous and nitrogen limited algal growth and that nonalgal particles affected light attenuation. These findings were further supported by the significant correlation among the values of TSI and hydrological factors.