This study proposes an integrated approach to assess the performance of a conjunctive-use surface and subsurface water system. System dynamics serves as the main framework of the proposed conjunctive-use model, simulating the interaction between surface and subsurface water and the impact of various conjunctive-use alternatives on the system as a whole. This study assumes natural groundwater recharge as a water source to the system, and estimates its volume using geographic information system (GIS) tools, a groundwater simulation model (MODFLOW), and a parameter identification model (UCODE). This study assesses various conjunctive-use alternatives and analyzes the frequency of water shortage to illustrate how the recharge rate affects water supply reliability under the conjunctive-use framework. Simulation results indicate that conjunctive-use with artificial recharge indeed reduces the frequency of extreme water shortages. Results also reveal that artificial recharge is necessary to maintain groundwater conservation without overusing river flow. Although this study focuses on southern Taiwan, the proposed concepts and procedure are applicable to other areas with a similar conjunctive-use framework.