River channel confluences are widespread in natural rivers. Understanding their unique hydrodynamic characteristics and contaminant transport rules may facilitate the rational and effective treatment of the water environment. In this study, we considered the Xitiaoxi River Basin as the research area, and a well-designed flume was established based on the extracted water system features. Hydrodynamically, in the Y-shaped confluence channel the flow velocity was easy to separate at the confluence, and a low flow velocity region appeared in the two branches. The spiral flow mainly flowed counterclockwise to the downstream region and the spiral trend increased as the discharge ratio decreased. The spiral flow and its effect on the transport and blending of contaminants were distinct between Y-shaped and asymmetrical river confluences. Based on the flow dynamics test, a set of pollutant discharge devices and a multi-point electrolytic conductivity meter were employed to research the mixing rule for pollutants. A high concentration zone for pollutants was likely to occur near the intersection, and the contaminant concentration band after the confluence was first compressed and then diffused. In particular, line source discharge in the left branch and the point source discharge in the inner bank of the left branch and in the outer bank of the right branch were dominant, and were conducive to the detection and treatment of pollutants.