Following the rapid development and urbanization in Yangtze River basin, in particular the operation of the Three Gorges Reservoir, the hydrological regime, sediment transport and water quality at the Yangtze outlet have changed dramatically, which significantly affected the estuarine ecosystem. Water quality deterioration, eutrophication and algal bloom become serious problems of the Yangtze estuary. The impoundment of the Three Gorges Reservoir has three stages: the first stage is 135 m in 2003, and the second stage is 156 m in 2006 and the final stage is 175 m in 2010. The impoundment of 175 m in 2010 makes the operation of the reservoir reach to the designed level. It is therefore valuable to investigate the consequent effects on the ecosystem of the downstream, especially the estuary. Based on the survey of hydro-environmental and phytoplankton data in the Yangtze estuary and its adjacent areas in August and November 2010 and May 2011, the paper analyzed the spatial-temporal features of dissolved oxygen (DO) and chlorophyll a (Chla), as well as the affecting mechanism after the impoundment level of the Three Gorges Reservoir reached to the final stage of 175 m. The results showed that in summer, the low DO area is in the turbid belt in surface layer, and the bottom layer exists oxygen depletion zone. In autumn and spring, the vertical profile of DO concentration is rather uniform from surface to bottom. To investigate the effect of stratification in summer, two typical points A3 and A5 are selected. In A3, DO and temperature decreases monotonically with the depth and Chla increases with depth; in A5 station, DO and Chla first decrease sharply with depth and then gradually increase after 20m depth. The difference of vertical profile between A3 and A5 is because of the stable stratification in A5. For Chla, there are two high value zones in summer and one in spring. In particular, in the north edge of the estuary outlet, the Chla concentration in the surface layer is very high, reaching to eutrophic level. With respect to vertical profile of Chla, the concentration in surface and bottom layers are higher than middle layer (thermocline) in summer, while in spring and autumn the concentration in surface layer is lower. In combining with previous studies, it is found that the low DO zone and the peak Chla contour line are moving toward inshore, which will affect the estuarine ecosystem. From the study, it can be concluded: (1) the maximum concentration of Chla can be in surface, middle or bottom, depending on the vertical stability of the water. The horizontal change of the hotpot is governed by the inflow discharge. (2) in the mixing zone, the peak of Chla concentration is closely correlated with nutrients. (3) near the outlet, the vertical profiles of Chla and DO are opposite, but in offshore area they are consistent. (4) after the impoundment of 175 m, the discharge and sediment as well as nutrients are further reduced, which will intensify the effects on Chla and DO features of the estuary.