The Three Gorges Reservoir (TGR) is one of the largest hydroelectric projects in the world, with significant impacts on the hydrology and ecology of the Yangtze River Basin. Understanding the effects of TGR operation on surrounding water systems, especially the Jingjiang Reach and Dongting Lake, is crucial for local water resources management and flood control. This study evaluated the impact of the TGR on water diversion in the Jingjiang Reach and outflow from Dongting Lake using observed data and sedimentation patterns before and after TGR operation. A coupled one-/two-demensional hydrodynamic model was developed to simulate hydrological processes. The relationship between TGR scheduling and Dongting Lake inflow and outflow across different periods was quantified. The results indicated that after TGR operation began, riverbed erosion significantly lowered tributary water levels under equivalent main stream flow. Lake inflow through the three Jingjiang Reach outlets increased during drawdown and water supplement periods but decreased during flood and impounding periods. Lake outflow increased during drawdown, flood, and water supplement periods but declined significantly during the impounding period. The contributions of factors varied considerably. Reservoir scheduling accounted for 328.86% of inflow changes at the Taiping outlet during the drawdown period but only 20.72% during the flood season. River topography changes contributed 157.41% to lake outflow changes during the drawdown period, but only 1.85% during the water supplement period. These findings enhance our understanding of river—lake system evolution and support improved management strategies.