In order to investigate the ecological effects of dredging on aquatic ecosystem in the different regions of the eastern Lake Taihu, the water, sediments and biological samples in eastern Lake Taihu (aquaculture lake region) and Xukou Bay (macrophytedominated region) were collected in August, 2012. Contents of nutrients and heavy metals in sediments and water quality parameters were measured, and the phytoplankton, zooplankton and benthos communities (including species composition, density and biomass) also were investigated. The results showed that dredging was a useful approach for lowering nutrients and heavy metals loading in sediments, but its effectiveness had gradually decreased with the end of dredging. The Hakanson potential ecological risk index also indicated that sediment dredging could reduce the extent of potential ecological risk. There were obvious differences between the effects of the dredging to water quality and aquatic organisms in different lake regions. The water quality had been improved in the dredged areas of the eastern Lake Taihu, and both density and biomass of the phytoplankton had been decreased compared with the un-dredged areas. The macrophyte and benthic communities had also been restored quickly in a short period. On the contrary, the sediment dredging in the macrophyte-dominated region of Xukou Bay destroyed the healthy macrophyte community, which caused the water quality deterioration and slow restoration of aquatic organism.