Based on analyses of the hydrodynamic parameters, turbidity, and temperature of water in the bay of the Meixi River, a typical tributary in the middle area of the Three Gorges Reservoir area, the characteristics of flow at the interface between the mainstream and the tributary during different operation stages of the Three Gorges Reservoir were investigated, and the factors influencing the flow characteristics and the influence of water exchange on the bay are discussed. The results show that the flow is bidirectional in the Meixi Estuary. Driven by the thermal density flow, the inertia of mainstream flow, and changes in the reservoir water level, the flow intensity at the interface and the structure and pattern of the interface between the inflow and outflow differed in different operation stages. The net flux is low(mostly below 100 m³/s), while the water exchange volume(from 314.17 to 535. 26 m³/s, about 4 to 40 times the net flux)is relatively large at the interface in the Meixi River Estuary because of the bidirectional flow. The mainstream inflow could reach the end of the perennial backwater zone even during the low-water level stage with minimum net flux.