Large shallow reservoirs control flooding, supply water, and protect the ecological environment, which are vital functions for societal development. As the largest artificial plain reservoir in China, Suyahu Reservoir is suffering from significant sedimentation and water quality deterioration in recent years. A three-dimensional (3-D) hydrodynamic and water quality model was developed based on the Environmental Fluid Dynamic Code (EFDC). The model was applied to seven scenarios for evaluating the response of in-reservoir hydrodynamics and water quality to the restoration measures, including expansion and sediment dredging project, external load reduction, and inflow regulation. The results show that: (1) the expansion and sediment dredging project has no notable improvement on the water quality of the reservoir; (2) the external load reduction can significantly improve the water quality of the reservoir; and (3) the optimal inflow condition occurred when the flows of Ru River’s two inlets were evenly distributed, and the hydrodynamics and water quality were best improved. Moreover, the increasing water exchange rate could not cause the same water quality improvement, showing that it may be unreliable to evaluate the effects of restoration measures using a single indicator. This study can provide useful information for developing and implementing effective restoration measures in large shallow reservoirs.