Abstract: As the largest freshwater lakes in China, the Poyang and Dongting Lakes enter a complicate coupling with the middle reach of Yangtze River, which plays a significant role in flood control and eco-environment protection. Based on the field flow-sediment and topography data, the leading factors to the characteristics of sediment erosion and deposition in both Lakes have been studied, of which the Three Gorges Reservoir is highlighted. The results indicate that the rate of siltation in both Lakes shows visibly slowdown to occasional erosion in the recent decade. The decrease of sedimentation rate in Dongting Lake is basically induced by the reduction of incoming sediment due to the operation of Three Gorges Reservoir, while the erosion dominated in Hukou reach of Poyang Lake is mainly caused by excessive sand mining rather than the Three Gorges Reservoir which still remains uncertain.