Phosphorus fate and transport in natural waters plays a crucial role in the ecology of rivers and reservoirs. In this paper, a coupled model of hydrodynamics, sediment transport, and phosphorus transport is established, in which the effects of sediment on phosphorus transport are considered in detail. Phosphorus adsorption is estimated using a mechanistic surface complexation model which is capable of simulating the adsorption characteristics under various aquatic chemistry conditions. The sediment dynamics are analyzed to evaluate the deposition and release of phosphorus at the bed surface. In addition, the aerobic layer and anaerobic layer of the sediments are distinguished to study the distribution of phosphorus between dissolved and particulate phases in the active sediment layer. The proposed model is applied to evaluate the effects of various operating rules on sediment and phosphorus retention in the Three Gorges Reservoir (TGR). Results show that the proposed model can reasonably reflect the phosphorus transport with sediment, and management scenarios that influence sediment retention will also influence the phosphorus balance in the TGR. However, modest operational changes which have only minor effects on sediment retention also have limited influence on the phosphorous balance.