We studied the impacts of Three Gorges Reservoir (TGR) on the sedimentation regimes in the downstream-linked two largest Chinese freshwater lakes, Lake Dongting and Lake Poyang. Our results indicate that up to 1.73 × 109 t sediment was retained in TGR from June 2003 to December 2014. This resulted in a 145.9 × 106 t yr-1 decline in the suspended sediment load at Zhicheng and a 16.8 × 106 t yr-1 lower sediment flow from Yangtze River to Lake Dongting, which partially explains the 13.4 × 106 t yr-1 lower sedimentation in Lake Dongting during the post-TGR period. Furthermore, TGR resulted in a 0.5 ± 0.3 m reduction of the multi-year mean water level at the Lake Poyang outlet Hukou, accelerating the suspended sediment export discharge from the lake. The reduced sedimentation in Lake Poyang during the post-TGR period was estimated to 6.3 × 106 t yr-1. We estimate that a monthly mean concentration of sediment flow from TGR below 0.60 kg m-3 will lead to erosion in Lake Dongting and Lake Poyang. Better regulation of TGR may extend the life expectancy of the two vanishing large lakes.