As agricultural non-point source runoff is transported to a wastewater treatment plant by the sewage interception trunk around Dianchi Lake, the total phosphorus(TP) concentration decreases along the way, often falling below the designed influent concentration at the trunk’s endpoint. This reduction can result in non-compliance with discharge standards. To explore the influence of key design parameters on endpoint TP concentration and provide technical guidance for sewage interception trunk design, this study focuses on granular phosphorus from agricultural runoff transported by a well-designed sewage interception trunk on the eastern bank of Dianchi Lake. Using the three-dimensional simulation software FLUENT, a multiphase flow model was constructed to stimulate the fluid flow process within the trunk. The influences of section shape, roughness, hydraulic diameter, and slope on the endpoint TP concentration were analyzed. Results show that the endpoint TP concentration is lowest for circular cross sections and highest for trapezoidal sections. As roughness increases, TP concentration rises across all section shapes, with the smallest variation range in rectangular sections, and the largest in circular sections. Increasing hydraulic diameter or slope results in increased or decreased TP concentration for rectangular or trapezoidal sections, while in circular sections, TP concentration either decreases or shows minimal change.