Typhoon Aere in 2004 induced severe sedimentation and loss of storage capacity of the Shihmen Reservoir in northern Taiwan. The resulting dramatic increase in the turbidity of the water seriously affected the water supply. To effectively maintain the stability of the water supply and maintain the reservoir’s storage capacity, the government of Taiwan began to plan and construct a series of improvement measures, such as a sediment flushing tunnel, the JhongJhuang Bank-Side Reservoir, and the Amuping Desilting Tunnel. However, previous studies only focused on the impact of the sediment flushing tunnel and the Amuping Desilting Tunnel on the downstream riverbed, and did not consider the possibility of increasing sediment discharge after the completion of the JhongJhuang Bank-Side Reservoir. In addition, climate change will cause the intensity of extreme rainfall to increase enormously in the future. That rainfall and extra sediment flushing will challenge the existing flood prevention facilities. Therefore, this study considered that the JhongJhuang Bank-Side Reservoir will increase sediment discharge of the Shihmen Reservoir, and used dynamical downscaling extreme typhoon data of climate change under the RCP 8.5 scenario to explore the flood prevention and riverbed migration of the main channels of the Dahan and Tamsui Rivers in the future. We used the rainfall–runoff model of Hydrologic Modeling System to simulate rainfall and runoff, and used the hydraulic and sediment transport model of CCHE1D to holistically simulate flood events and consequent river scouring and deposition behaviors. Our results showed that the projected peak discharge during the late 21st century (2075 to 2099) will be at least 50% higher than that during the baseline (1979 to 2003) period. In terms of flood prevention, the potential of overbank flooding will increase in the downstream area, and the trend of long-term change in the riverbed will be dominated by degradation (-0.489 ± 0.743 m) in the future. The improvement measures will have a limited impact on riverbed migration (0.011 ± 0.094 m) in the Dahan and Tamsui Rivers. After the operation of the JhongJhuang Bank-Side Reservoir, the Shihmen Reservoir is expected to increase the sediment discharge ratio by 70% during floods, and it will not cause excessive water turbidity that may affect downstream water supply.