Sediment dredging has a great effect on the control of lake internal loading and is one of the important methods for lake internal loading management. In this study, the dredged area of Taihu Lake was used as the main object. An estimation of the reduction in whole lake internal loading of Taihu Lake in decade years was carried out. At the same time, we evaluated the effect of sediment dredging on the control of internal loading in the northern area of Taihu Lake (Zhushan Bay and Meiliang Bay). The results indicated that a total of 42 million cubes of sediment was dredged from Taihu Lake, and the total nitrogen, total phosphorus, and organic matter in the dredged sediment was estimated to be approximately 6.26×104 tons, 1.83×104 tons, and 11.7×105 tons, respectively. This was roughly equal to the 20 years of external loading pollution accumulated in Taihu Lake. From a long-term perspective, sediment dredging could effectively increase the water quality of Meiliang Bay within five years and that where the external loading has been controlled effectively. However, the water quality of Meiliang Bay subsequently rebounded, but dredging still reduced the nitrogen and phosphorus content in surface sediment. On the contrary, dredging could not effectively control the internal loading of Zhushan Bay, which still had a large input of external loading. The amount of sediment internal loading recovered to the original level of the pre-dredging period. In a six-year-long period of continuous monitoring of the benthic organism community of Zhushan Bay, the results indicated that sediment dredging could cause negative effects on sediment dredging initially, but the density and biomass of the benthic organisms in the dredged area had later been recovered to the un-dredged level. There was no difference between the dredged and un-dredged areas with regard to the diversity indices of benthic organisms. The results of this study indicated that sediment dredging can effectively control the lake internal loading. However, the maintenance period of dredging effects was related closely to the input intensity of the external loading. In addition, sediment dredging did not have a large influence on the benthic organism community and could recover to the original level depending on self-recovery.