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Anthropogenic contamination and excessive water consumption endanger an overexploitation of groundwater, which causes groundwater mineralization in coastal aquifer of Lebna area. Consequently, the salinity of groundwater reserves increases and creates big economic, agricultural, and social problems. Moreover, agricultural activities are the main source of nitrate, sulfate, and potassium ions and contribute to groundwater salinization and contamination with increasing chloride and nitrate concentrations. The objectives of this research are to determine the main source of groundwater salinization in coastal aquifer of Lebna area to not confuse between seawater intrusion and fertilizer effects and to determine the salinity effects on the ecosystem. To reach this goal, several geological tools and hydrogeological data are used in combination with geochemical and geophysical methods.