Discovering groundwater resources in a fault-controlled aquifer system appears to be a viable solution to water scarcity in the mountainous areas of Taiwan. Regoliths, fractured bedrock, and faults commonly exist in such aquifer systems. To investigate the groundwater behavior in the three subsurface media, a 3-D hybrid model (equivalent porous media/discrete fracture network) involving various in situ investigation techniques (borehole drilling, outcrop investigation, borehole televiewer logging, sonic logging, and downhole hydraulic tests) was proposed to assess the hydraulic properties and groundwater storage of the Dili fault zone of Central Taiwan and its surrounding formations. Subsequently, the model was verified through a case study of a simple fracture network. Based on the validated model, flow path analysis was successfully performed to reveal the hydrogeological role of the fault zone, which acts as a conduit for groundwater flow. To ensure the simulated result regarding the hydraulic properties of the fault zone, this study proposes three additional cross-checking techniques, namely stable water isotopes, derivative plots of pumping test data, and identification of hydraulic gradients. The results of the investigation show that the hydraulic properties of the fault zone obtained by the three approaches are consistent with those determined by the numerical method, and the use of the three cross-checking techniques has been confirmed to be suitable for effectively exploring the hydraulic properties of a fault because the site characterization data are insufficient. Finally, the developed hybrid model was used to calculate the groundwater storage of each geological zone, indicating its great potential for the development of groundwater resources in the study area. Therefore, this study integrates in situ investigation techniques, numerical models, and three evaluation approaches of fault zone hydrogeology to construct a systematic, feasible, and applicable exploration methodology that can be employed for groundwater resource exploration in a fault-dominated aquifer system.