The construction of the New Galala City besides great mining (e.g., konoozmisr) and Seawater Reverse Osmosis Desalination Plant projects in the semiarid Gulf of Suez region of Egypt increases the demand for groundwater resources. So, the current research provides integrated stratigraphical, hydrogeochemical, and geophysical studies to investigate the shallow groundwater aquifers in Wadi Araba area on the western side of the Gulf of Suez. The stratigraphic column starts with pre-Cambrian basement rocks which are non-conformably overlain by sedimentary succession of Phanerozoic Erathem. A detailed land magnetic profile has been conducted and processed to estimate the aquifer’s geometrical parameters. This includes the subsurface spatial extension and thickness to delineate the prevailed subsurface structures in the study area. Lithostratigraphically, these aquifers are represented by the Paleozoic- lower Cretaceous siliciclastic-dominated sediments of the Nubia Group and fractured carbonate-dominated facies of the upper Cretaceous Galala Formation. Lithological characters, sedimentary facies (fluvial to shallow and open marine), microfacies types, and diagenesis processes (e.g., compaction, cementation, dissolution, and fracturing) are the main factors that affect the quality of the shallow aquifers in the study area. The main microfacies of the studied aquifers are quartz arenite, subarkose, sublitharenite, mudstone/wackestone, and packstone/grainstone. These facies are characterized by different primary and secondary porosities. According to the water sampling standard methods, nineteen groundwater samples were collected from the available hand-dug wells and springs from the Nubian sandstone aquifer and the Upper Cretaceous aquifer, respectively. Inductively coupled plasma–mass spectrometry (ICP–MS), titration, spectrophotometer and a flame photometer were used to obtain a complete chemical analysis. The results of hydrochemical analyses indicated that total dissolved solids (TDS) and concentrations of major ions as well in the lower Cretaceous aquifer increase toward the Gulf of Suez and in general higher than that of springs of the Upper Cretaceous Aquifer. The predominant factors influencing groundwater chemistry include seawater intrusion, evaporation, mineral alteration, dissolution of fossils, and ion exchange. Groundwater in the study area is unsuitable for drinking except in one sample and moderately suitable for irrigation with caution for higher salinity in samples located near the Gulf of Suez.