Abstract: With the rapid development of industry and agriculture, river water pollution problems are becoming more and more serious. The phenomenon of water flow confluence is common in river systems. Due to the complex hydraulic characteristics of the intersection, the influx of highly concentrated pollutants from branch channels can accumulate in the downstream of the main channel, causing river water pollution and seriously threatening the water safety of downstream regions. Aiming at the water quality pollution of the confluence caused by tributary discharge, a two-dimensional hydrodynamic and water quality coupling model of the 90° equal-width open channel confluence is established based on the hydrodynamic and water quality model software Delft3D. The model parameters are calibrated through comparison and verification with physical model experiments in existing studies. The study proposes that the engineering measures of arranging submerged dams near the open channel intersection can intensify the convection of the flow, enhance the mixing of pollutants and reduce the concentration of pollutants, so as to solve the problem of water pollution near river confluences. A total of 14 arrangements of different submerged dam locations, lengths, and heights are numerically simulated. Then the pollutant distribution maps and flow field distribution maps under each working condition has been obtained, and the variation coefficient and extreme value of pollutant concentration in each section are calculated for analysis. The research findings show that the arrangement of submerged dams near the confluence can accelerate the mixing of pollutants, thereby reducing the extreme value of pollutant concentration. The main mechanism for the submerged dams to accelerate the mixing and diffusion of pollutants is that the transverse velocity zone and recirculation zone generated by the submerged dam intensify the flow convection effect, promoting the mixing of pollutants. The arrangement of submerged dams on the right bank of the main channel downstream of the confluence has a better effect on reducing the concentration of pollutants than the arrangement of submerged dams on the left bank. Among the simulated conditions, pollutant concentration can be most significantly reduced when the length of the submerged dam is one-half the width of the river.The higher the submerged dam, the better the effect of reducing the extreme value of pollutant concentration. The coefficient of pollutant concentration variation can be reduced by 46%, and the maximum pollutant concentration value can be reduced by 33% under the appropriate submerged dam arrangement condition compared to the baseline condition without submerged dams. When the submerged dam is arranged across the river width, the generated transverse flow velocity area is located on the bank, which has limited effects on the mixing of pollutants. The research conclusions can provide a scientific basis for pollution control in converging rivers.