This study integrates Very Low Frequency Electromagnetic (VLF-EM) and Time-Domain Electromagnetic (TDEM) methods to characterise subsurface geological structures and aquifer conditions in the New Nubariya-2 City, Egypt. VLF-EM analysis, enhanced by Fraser filtering and Karous-Hjelt pseudo-sections, identified nineteen conductive linear anomalies (F1–F19) interpreted as fracture zones. TDEM 1D inversion validated several of these anomalies and delineated four distinct geoelectric layers: a heterogeneous surface layer composed of dry sands, silts, clay, or gravel (5–216 Ω·m), a low-resistivity clay layer (1.2–2.4 Ω·m) with thicknesses of 28–71 m, a water-saturated sand aquifer (13–33 Ω·m) with depths increasing from 34 m in the east to approximately 104 m in the northwest, and a basal clayey sand formation (3.7–9.6 Ω·m). The southeastern and northwestern regions were identified as optimal for well drilling due to greater aquifer thickness, higher resistivity, and the presence of deep water-bearing fracture zones. These findings enhance the understanding of groundwater resources in the West Nile Delta and provide valuable insights for urban planning and water resource management in the New Nubariya-2 City.