This paper deals with the impact of soluble salts on the deterioration of wall paintings in the region of Wadi El Natrun in Egypt, including the identification of the building materials and pigments used. For this purpose we used XRD analysis which proved that the green pigment in the Church of the Virgin, Wadi El Natrun is a mix of malachite and hydrocerussite, and the black pigment is graphite. The results proved that the building materials (stones, mortar, and plaster) in Wadi El Natrun are affected by ground water as they have the same soluble salts at different concentrations. The Wadi El Natrun lakes are the native source of natron salt, which has been used in mummification techniques. Soda lakes represent the major types of naturally occurring highly alkaline environments. The factors leading to the formation of the alkaline saline deposits may be divided into climatic, geological, and topographical. Climatic and topographical factors control the amount of water entering the system as rainfall or surface runoff and the amount leaving by evaporation. Geochemical factors determine which ions enter the system. Solutions of carbon dioxide result in the formation of a weak carbonic acid, which dissolutes the mineral components of the surrounding rocks and archaeological buildings, leading to their ion release.