Due to the booming socio-economic developments, along with the evitable climate change impacts, water resources management has become more challenging in Taiwan. 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 of water resources and improvements after implementing adaption measures. Each indicator was presented with 3 grades, namely low, medium and high. Vulnerability and resilience of water resources of Tainan City in southern Taiwan were evaluated. Insufficient capacities of water supply facilities are the major weakness causing low resilience. Flexibility of allocating water resources is limited by substantial agricultural water demands. A total of 9 adaption measures and combinations of measures were assessed. Implementation of desalination plants can steadily supply public water to shorten system failure duration. Although agriculture 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 adjustment of cropping systems have cross-spatial flexibilities. Combinations of desalination, reservoir, and public water conservation provide the most beneficial effects in reducing the impact of climate change.