In Taiwan, the seasonal distribution of rainfall is not even. The most rainfall centralizes in summer by typhoon, especially in southern Taiwan. Because the central mountain blocks monsoon, there is less rainfall in winter. The characteristics of rainfall influences the water supply of a reservoir in Taiwan. When a reservoir cannot satisfy water demands, how to use groundwater properly as a supplement source to mitigate the deficiency of water supply is important for the sustainable water resources management. First, this study adopts the concept of reservoir operational rule curves to formulate and classify water supply strategies based on reservoir and groundwater levels. After that, an optimization model for conjunctive uses of surface water and groundwater is constructed in this study to reduce the possibly deficiency of water supply. The objective of the model is to minimize the total water deficits, and then a heuristic algorithm is integrated to optimize the classification criteria and associated management strategies. This study is expected to apply the proposed research processes to develop appropriate management strategies for conjunctive use of surface water and groundwater and meantime to maintain the sustainability of water resources.