Knowledge of the distribution of contaminants at channel confluences is critical for understanding their transport and dwelling at river networks where flow confluences constitute the key nodes. Flume experiments were conducted to study the distribution of phosphorus adsorption in surface sediment under complex hydrodynamics at channel confluences. The influence of the discharge ratio of the tributary discharge to the main stream discharge was also investigated. The results showed that the horizontal velocity and vertical velocity of flow are the dominant factors affecting the distribution of phosphorus adsorption. Flows with a larger horizontal velocity are not beneficial to phosphorus adsorption on sediment and thus low- and high-adsorption strips of phosphorus occur in the maximum velocity zone and the flow separation zone, respectively. Downwelling flows are beneficial to phosphorus adsorption on sediment as they can enhance phosphorus exchange between overlying water and the bed sediment. A small flow penetration with a small discharge ratio causes a decrease in vertical velocity in the separation zone as well as the strong intrusion of a helical cell into the bottom of this zone, which results in an increase in horizontal velocity near the bed and consequently the phosphorus adsorption is largely restricted.