Water resources management has become more challenging in Taiwan due to rapid socio-economic development and the complications of climate change. This study developed a systematic procedure for assessing water resources vulnerability and resilience with an integrated tool, TaiWAP, including climate change scenarios, a weather generator, a hydrological model, and system dynamic models. Five assessment indicators, including two for vulnerability, two for resilience, and one for availability were used to quantify changes in water resources and improvements after implementing adaption measures. Each indicator was presented with 3 grades, namely low, medium, and high. Water resources vulnerability and resilience for Tainan City in southern Taiwan were evaluated. Insufficient water supply facilities capacity is the major weakness causing low resilience. Water resources allocation flexibility is limited by substantial agricultural water demands. A total of 9 adaption measures and combinations of measures were assessed. Desalination plant implementation can steadily supply public water to lessen system failure duration. Although agricultural water conservation and fallow land can greatly reduce water demand, fallow compensation is a potential cost. When food security is considered, reducing irrigation leakage will be a better adaption measure to both water and agriculture stakeholders. Both agriculture water conservation and cropping systems adjustment have cross-spatial flexibilities. The combination of desalination, reservoirs and public water conservation provide the most beneficial effects in reducing climate change impact.