Geological structures introduce heterogeneity along deformed strata, which in turn exert a strong control on regional groundwater occurrences and water flow. We developed and applied procedures of structural, borehole and direct current resistivity (DCR) data to (1) figure out a reliable structural model of a fault-related dome, (2) visualize the relationship between structural complexity and aquifers geometry and (3) characterize the fault damage zones and its related sealing potentialities. The present approach was applied at the northern Eastern Desert, Egypt, considering its complex deformation history. To alleviate the uncertainties and artifacts in solving the DCR inverse problem, advanced and non-conventional inversion schemes were applied. Moreover, fault seal potentialities were assessed by applying the shale gouge ratio (SGR) estimation to predict the groundwater pathway flow. The main findings include: (a) The DCR measurements can be considered as a complementary tool to visualize the relationship between subsurface structures and aquifers geometry at highly deformed areas; (b) detailed surface structural data analysis combined with sophisticated inversion algorithms application can increase the reliability of the constructed geo-electrical cross sections for deep and large-scale geological surveys; and (c) the structural modeling of geological units and faults distribution contributes to clarify hydrogeological settings and aquifers connectivity. The approach can be readily applied elsewhere, as long as detailed structural analysis, geometric parameters and high-resolution DCR resistivity data are available.