Technical Abstract: The Soil and Water Assessment Tool (SWAT) is widely used to predict the fate and transport of phosphorus (P) from the landscape through streams and rivers. However, the current instream P model may not be suitable for many stream systems, particularly those dominated by attached algae and impacted by point sources. In this research, we developed an alternative model based on the Equilibrium P Concentration (EPC) concept coupled with a particulate scour and deposition model. This model was applied to the Illinois River Watershed in Oklahoma, a basin influenced by waste water treatment plant (WWTP) discharges and extensive poultry litter application. The model was calibrated and validated using measured data. Highly variable instream P concentrations and EPC values were predicted both spatially and temporally. The model also predicted the gradual storage of P in streambed sediments and the resuspension of this P during periodic high flow flushing events. WWTPs were predicted to have a profound effect on P dynamics in the Illinois River due to their constant discharge even under base flow conditions. A better understanding of P dynamics in stream systems using the revised model may lead to the development of more effective mitigation strategies to control the impact of P from both point and nonpoint sources.