Halayieb area is located at the southeastern corner on the border between Egypt and Sudan. The area has very important strategic aspects to Egypt. Groundwater is the only source of fresh water in the area. The hydrogeochemical characterizations of groundwater in the area were carried out, to assess the quality of groundwater for its suitability for drinking and irrigation purposes. Geologically the Precambrian rocks underlain the Mesozoic sandstone and Tertiary marine sediments. The groundwater of the area is recorded at the Miocene sedimentary succession and the fractured basement aquifers with a maximum water depth of 26.5 m from the ground surface. Groundwater quality is mostly saline caused by the sources of geogenic, anthropogenic, and marine origin of the water bearing formations. The resulting groundwater is characterized by Na+ > Ca2+ > Mg2+/Cl− > HCO 3 − > SO 4 2− : Na+ > Ca2+ > K+/SO 4 2− > Cl− > HCO 3 − facies, following the topographical and water flow-path conditions. The hydrochemical facies in this area fall in the field of NaCl type and the hydrogeochemical signatures indicated active hydrolysis and dissolution process of Ca-bearing minerals of the basement rocks and some sodium is lost, most probably through reverse ion exchange. Enrichment of Mn+ in some wells is regarded to the mining activity for manganese ores in the area. Groundwater quality is mostly not suitable for drinking purposes. For irrigation, the groundwater is mostly suitable in regard to the residual sodium carbonate and the magnesium hazard. According to the water quality assessment using United States salinity laboratory (USLL) diagram, most water samples located in category C3–S2, C3–S3, C3–S4, C4–S2 highlighting high to very high salinity hazard and medium to very high sodium content class. Most of the groundwater samples that are located away from the shoreline are suitable for livestock and poultry consumption. High salinity contents in the study area create severe problems for using water supplies and for future exploitation.