The effects of sediment dredging events on the aquatic ecosystem of Shuangqiao River in Chaohu Basin were researched in the present study, a one-year investigation on the aquatic ecosystem operated in the river. The water quality, the crustacean zooplankton community and the biodiversity index were compared and analyzed pre-with post-dredging. Our results indicated that:The sediment dredging events improved the water quality of Shuangqiao River significantly, and the concentration of nitrogen (N)and phosphorus (P)decreased by 48.09% and 19.09%, respectively. The sediment dredging events had a significant influence on the crustacean zooplankton community, the biomass of crustacean zooplankton decreased from 1.86 mg/L to 0.25 mg/L, which declined by 86.40%. The biodiversity index was mainly affected by sediment dredging and season. There's significant relationships between crustacean zooplankton and environment factors:pH, temperature, ammonium, nitrate, total dissolved nitrogen, total nitrogen and nitrogen:phosphorus ratio were positive to the biomass of crustacean zooplankton. Our results suggested that the sediment dredging would reduce the internal nutrients of river significantly. Furthermore, the sediment dredging events had a significant effect on the crustacean zooplankton community. The aquatic ecosystems of river would be healthy and safety by the operation of sediment dredging. Therefore, the sediment dredging would be beneficial for the aquatic ecosystem, while the eutrophication management of river was not only attribute to the removal of urban external pollution, but also to the exogenous pollution, especially for the reduction of N input.