Egypt is grappling with water scarcity challenges, which are exacerbated by extensive urban development in arid coastal regions with rugged terrain. Although desalinated water is an alternative source in the remote Halayeib region of Southeast Egypt, its cost increases reliance on groundwater from the intricate aquifers. This study aims to accurately delineate hydro-structural features, known as lineaments, and assess their impact on the groundwater conditions in this promising region. This integrated approach involves the assessment of various spaceborne sensors, including optical (Landsat 8), Digital Elevation Models (ALOS and ASTER-DEMs), and radar (Sentinel-1), using geospatial and geostatistical techniques within the Geographic Information System (GIS). Radar-based sensors, particularly the Sentinel-1A vertical–vertical (S1A VV) polarization, outperform all other datasets in extracting lineaments, yielding 4883 lineaments that correspond to the regional geological faults. These lineaments trend in NE–SW, NNE–SSW, NW–SE, and E-W directions. The results also indicated that both digital elevation models (DEMs) were less effective, showing different orientations with azimuth angles. S1A VV proved to be highly effective in identifying subsurface fractured hard rock terrains beneath thin sedimentary covers, especially in the flat coastal area of Wadi Serimatai, where they intersected natural drainage pathways. Geoelectrical sections confirmed that there are orthogonal subsurface faults extending from fractured basement aquifers to near-surface layers. These faults align with the NE-SW and NNE-SSW directions observed in S1A VV lineaments. Geostatistical analysis revealed that S1A VV structural lineaments, lithological, and hydrogeological factors influence the occurrence of groundwater. This emphasizes the structural control over groundwater and its significant impact on water flow and storage. The study provides valuable insights for groundwater management, guiding decisions related to the development of groundwater resources.