This study investigates groundwater resources in the El-Omayed area on the northwestern coast of Egypt. The aim is to assess the extent and severity of saltwater intrusion in the shallow aquifer system, as well as its potential impacts on groundwater resources. A combined geophysical and hydrochemical approach was adopted in this investigation. Across the study area, 32 vertical electrical soundings were conducted, along with two electrical resistivity tomography profiles. Sixteen water samples were collected, and then chemically analyzed to evaluate water quality, seawater intrusion, and source of salinity. The results of geophysical interpretation revealed the existence of a thin, shallow freshwater-bearing layer (42–95 Ω.m), predominantly situated in the central parts of the area, followed by saltwater saturated layers of (0.9–2.1 Ω.m) affected by the Mediterranean Sea invasion. The eastern portion of the aquifer also recorded a relatively high seawater intrusion. As evidenced by the actual data gathered from drilled wells, the study area can be divided into three distinct zones: fresh, brackish, and saltwater zones. The study identified the most suitable sites to establish new groundwater wells, in addition to identifying the source of salinity through the investigation of the geochemical properties of water samples.