Abstract: Because of the Three Gorges Reservoir impoundment, the riverbed downstream of the dam has been experiencing scouring. This has resulted in changes to the stage—discharge relationship of the hydrological cross-sections. Based on the daily flow and sediment data from 2003 to 2022, we analyzed the stage—discharge relationship for a number of typical hydrological stations and proposed a new method to calculate water level changes due to the confluence. This novel approach can reveal the mechanism of the impact of tributary inflow on mainstream water levels. The stage—discharge curve indicates a clear threshold for the flow rate. When the flow rate was less than this threshold, the water level continued to decrease; when the flow rate exceeded this threshold, the water level varied significantly without a distinct pattern. As a result of the confluence effect, a given flow rate could correspond to different water levels, making it difficult to use flow rate as a factor to determine the water level. The proposed method was validated using field data and can quantify the key factors that influence the degree and range of the backwater effect. Roughness increment caused by erosion in the riverbed because of the Three Gorges Reservoir impoundment can increase the range of the confluence backwater effect, causing abnormally high flood levels in some years. This study can provide a theoretical basis and technical support for flood control in the middle and lower reaches of the Yangtze River.