This article presents the modeling of hydrothermal characteristics and suspended solids in a long and large-volume reservoir with a highly fluctuating water level. A laterally averaged two-dimensional hydrothermal and water quality model was configured for the Shihmen Reservoir in northern Taiwan. The model was validated with measured data of water surface elevation, water temperature, and concentration of suspended solids in 2006. The results show that the numerical model was able to reproduce the measured data. The validated model was then used to investigate the effects of water withdrawal schemes at different depths and to estimate the residence time in the reservoir. When water is withdrawn from a great depth, the relatively warm water from the upper layers can replace that in the deep layers, thereby facilitating heat transfer from the surface to the deeper layer. Bottom-water withdrawal results in a lower concentration of suspended solids compared with withdrawal from depths of 20 and 40 m. The simulated results show that the residence time is approximately 154 days in the Shihmen Reservoir.