The effect of environmental dredging projects in China has received wide attention with many case studies. However, little care was paid for dredging in stratified water sources. How to evaluate the effects and then control sensitive parameters is still an unsolved problem. Tongjiqiao Reservoir, a typical deep reservoir as well as a drinking water source, was chosen as a long-term case study. Result shows that Tongjiqiao Reservoir mainly reached water quality standard Ⅲ. Within half a year after the project, environmental dredging partially reduced near-dam total nitrogen (TN) concentration to 56%-87% of the past level, but 1.87-5.12 times as high as before in total phosphorus (TP) concentration for near-dam area. Turbidity, TN, TP and manganese (Mn) concentrations were sensitive parameters. The change of TP was closely related to turbidity caused by sediment disturbance. Besides, exorbitant Mn concentration at the bottom of the reservoir was related to both the exorbitant Mn in after-dredging surface sediments, where the highest content located in the near-dam area, reaching 1251.25 mg/kg. The seasonal stratification caused anaerobic conditions in deep water area. Therefore, environmental dredging of deep source ought to consider the impact of both sediment disturbance during dredging and thermocline after dredging.