Groundwater recharge characteristics of a karst plateau which plays an important role in the recharge of a regionally important highly productive karst aquifer was revealed by combined application of Electrical Resistivity Tomography (ERT) and Square Array Configuration methods. A forward model of targeted karst features and geological structures constructed prior to ERT survey enabled a more comprehensive and more reliable interpretation of the real data. The transition between the anomalies resulted from different structures were sharp and the artifacts were distinct in the inverted sections of the synthetic data whereas a smoother transition was observed between different types of anomalies in the real data and the artifacts were harder to be distinguished from the anomalies related to the real subsurface structures. The air-filled karst shafts and caves inside the Triassic aged marbles resulted in high resistivity anomalies approximately between 3000 and 6000 Ωm. On the other hand, clay rich soil zones and water bearing fissure networks led to low resistivity anomalies ranged between 100 and 400 Ωm. ERT survey detected various well karstified fast recharge zones and indicated that the network of karstified zones dipped through northeast (NE). The method also pointed out that nonkarstified fissure networks and thick layers (10–15 m) of clay rich soil zones leading to a lagged recharge existed some regions in the plateau. Square Array Configuration survey signified that dominant fracture zones existed in SW-NE and NW-SE directions and indicated that the faults and fractures in the region (SE-NW and SW-NE oriented) extended deep inside the karst aquifer. Overall evaluation of ERT and Square Array Configuration results enabled the determination of fast and slow recharge zone distribution throughout the karst plateau and thus, distinguished the highly sensitive regions in karst plateau for groundwater contamination. Finally, this study showed that combined application of Square Array Configuration and ERT surveys could successivley characterize groundwater recharge in a complex karst terrain and could constitute a supportive method for revealing the spatial vulnerability differences of a karst region to groundwater contamination.