Water availability and quality have been identified as essential for human development, encompassing sectors such as agriculture, industry, and public supply. This study adopted a multidisciplinary approach, integrating geophysical methods, focusing on electrical resistivity tomography, and structural surveys to investigate a confined fractured aquifer in the Serra do Itaqueri region, known for its complex and diverse geology. Located on the eastern edge of the Paraná Basin, this region exhibited rugged terrain predominantly composed of sandstones from the Botucatu Formation and basalts from the Serra Geral Formation, in addition to fracture and fault systems controlling subsurface flow. The results indicated recharge and discharge zones associated with tectonic structures, such as a NE-SW-oriented reverse fault that acted as a hydraulic barrier in certain sections. 2D and 3D electrical resistivity models revealed significant contrasts between saturated and unsaturated zones, emphasizing the recharge zone’s vulnerability to human activities. The results underscored the importance of electrical tomography as a tool for aquifer characterization and the need for conservation strategies to preserve water resources in environmentally fragile areas.