The study area is situated in the Qelabshowah–Belqas region, known for its Quaternary deposits. This research aims to demonstrate the two-dimensional (2D) variation of subsurface layers and salinity distribution using geoelectrical data, hydrochemical analysis, and geostatistical analysis. DC resistivity measurements were taken at fifteen vertical electrical sounding (VES) survey points using a Schlumberger array (AB/2 = 100 m) along three profiles. In addition, an electrical resistivity tomography (ERT) survey was conducted with a dipole–dipole array across one profile. Seven surface water samples were collected in the area. From the 1D and 2D inversion of VES and ERT data sets, three-to-four geoelectric layers were identified, including unconsolidated surface deposits, saturated clayey sand, saturated sand, and a salt-rich layer. The 2D inversion of VES data revealed an ancient salt-rich layer deposited in swampy conditions over a conductive wet sand layer along profile one due to salt mineral infiltration and dissolution. The 2D inversion of ERT data showed accurate lateral geometric accuracy compared to the 2D inversion of VES data, highlighting geological features, such as caves in the second layer and a buried water canal on the ground surface. Surface water samples showed high salinity levels with sodium hazards, indicating an Na–Cl composition. Geoelectric and hydrochemical data sets were geostatistically analyzed using spherical variogram supported ordinary Kriging interpolation. The analysis indicated weak to moderate spatial dependency for true resistivity parameters, while sodium content (SC) and permeability index (PI) showed strong spatial correlation. The 2D spatial distribution resistivity maps based on the 1D inversion of VES data displayed a general decrease in resistivity with depth, likely due to clay minerals or moist soil in the second layer and saline irrigation water infiltration in the third layer. The 2D spatial distribution of SC and PI showed a high concentration zone, posing a potential risk to agricultural crops regardless of soil permeability. It is recommended to use these maps when cultivating plants that can tolerate high sodium levels during the reclamation process.