This paper aims to propose a decision support system (DSS) for evaluating the climate change impacts on water supply–demand and inundation; and assessing the risks for water shortage and inundation under future scenarios. The proposed DSS framework is universal and flexible, which comprises five modules integrated by a geographic information system platform, including the modules of (1) scenario rainfall and temperature projection under climate change, (2) impact assessment of water supply–demand, (3) impact assessment of inundation, (4) assessment of vulnerability and risk, and (5) adaptation strategy. A case study in southern Taiwan was performed to demonstrate how the DSS provides information on the climate change impacts and risks under future scenarios. The information is beneficial to the authorities of water resources management for understanding the spatial risks for water shortage and inundation, and planning suitable adaptation strategies for the locations with larger risks.