The water and sediment conditions of branching rivers are complex and changeable. In order to ensure the stability of the channel and the navigation safety of ships, navigation structures are usually arranged at the shore side of one of the branches when designing the layout of the water conservancy project of a branching river. Due to the limitation of engineering constructions, it is necessary to arrange the navigation structures in the middle of the branching river, which disturbs the flow patterns and obstruct the navigation from sediment deposition. Based on the poor navigation conditions of the existing locks of Taoyuan Junction, which are arranged in the confluence section of the island end of the branching river section, the experimental study on the characteristics of water and sediment obstruction in the downstream gate area of the lock was carried out by combining the integrated fixed-bed flow, fixed-bed sediment transport and remote control self-propelled ship model tests. The results showed that the flow condition was the underlying cause of flow obstruction and sedimentation obstruction. The left and right branch drainages of water flow in the confluence formed a sudden unilateral enlargement or mixed flows, causing a bad flow regime and bedload sediment silting obstruction at the entrance area of the downstream section. Therefore, branching river lock arrangement should be carefully considered in the river.