Groundwater resources are unique water supply in arid regions such as Sinai Desert and Negev Desert that locates along the eastern border of Egypt. The Eastern Mediterranean Aquifer (EMA) is crossing the border between Egypt and Gaza Strip. It is located in the coastal plain, along the eastern shore of the Mediterranean Sea. It is delineated on the World Map of Transboundary Aquifer Systems and depicted with number 502 (Struckmeier et al., 2006). It is defined on the world map as priority aquifer for water stress areas (Fig. 1). It is locally known as Kurkar Group (Calcareous sandstone, Sandy clay, Calcareous, clayey sandstone, Sandy limestone). Groundwater is recharged by precipitation at an average volume of 372 MCM/yr and generally flows westward toward the Mediterranean Sea. Groundwater is withdrawn primarily from sand, gravel, and Calcareous sandstone of Quaternary age (USGS, 1998). Groundwater levels are influenced by precipitation and pumping and generally fluctuate about 1–2 meters per year. Groundwater is generally of fresh water quality, with chloride concentrations between 50 and 250 mg/L. The EMA in Egypt has been greatly affected by pollution across the boundaries (Geriesh et al., 2004). The political situation is not stable and residents along both sides have continues emerging and unstable socio-economic conditions. The local inhabitants are greatly affected by deterioration of groundwater resources and spoiling soil environment. The EMA has been greatly deteriorated due to the continuous bombing for the border line. These aggressive activities may exaggerate the pollution of this aquifer that is used in Egypt for supplying drinking water and for irrigation.