The computational modeling of flow and sediment transport at the confluence of the Kankakee and the Iroquois rivers was studied. The effectiveness of engineering alternatives on reducing sedimentation at the confluence was also discussed. The EnSed2D model was applied to the simulation of suspended sediment transport system. The hydrodynamic model simulated flow field and suspended sediment concentration distribution under different alternative management scenarios. The study chose the average flow discharge as the simulation discharge to determine the most cost-effective restoration method through evaluating and comparing flow fields, suspended sediment distribution, and the sedimentation patterns.