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In this study, the distribution of the chemical constituents (major, minor, and trace elements) is determined in different localities in Egypt’s western desert oases, i.e., Bahariya, Farafra, Bahrean, Siwa, El-Gara, and Al-Jaghbub oases. The Nubian Sandstone Aquifer (NSA) is shared between all oases; however, the Limestone Aquifer (LA) is shared only between the western oases, i.e., Bahrean, Siwa, El-Gara, and Al-Jaghbub. The LA is usually located above NSA in Egypt’s western desert. The results indicate notable difference in chemical characteristics between the LA and the NSA waters. Under furrow surface irrigation systems that are commonly used in the Bahariya and Farafra oases, negligible potential for harmful effects on soils and plants is anticipated. However, in case of using drip or sprinkler irrigation systems, the iron and manganese identified in groundwater may precipitate, causing blockages to occur. The LA waters salinity is found to be higher than NSA and above acceptable level for irrigation. Besides, salinity, chloride, and water sodicity make this water unsuitable for irrigation. Durov and piper diagrams reveal that the majority of investigated waters were calcium-magnesium sulfate water type corresponding the Bahariya and Farafra, and sodium, chloride, and sulfate water type corresponding the Siwa, Bahrean, El-Gara, and Al-Jaghbub waters. The saturation indices for minerals indicated that most studied LA waters were undersaturated for halite; however, the NSA waters were saturated with respect to aragonite, calcite, and dolomite.