The Western Desert is considered as one of the most promising areas for groundwater resource and development in Egypt. The Eocene carbonate aquifer is one of the most exploited aquifers for development in the Egyptian Western Desert, especially in the area west of El-Minia in central Egypt. The present study aims to assess the hydrochemistry of the Eocene carbonate aquifer and the possible recharge sources to this aquifer in the western desert west of El-Minia district. Fifteen groundwater samples from the Eocene carbonate aquifer were analyzed for major ions, heavy metals, oxygen-18, and deuterium to assess the hydrochemistry and isotopic compositions in this area. TDS concentrations ranged from 510 to 1408 mg/l. However, the cluster analysis of the Eocene groundwater samples in the present work, reveals two main groups (A and B) with different chemical and isotopic characteristics. The chemical composition of the studied samples showed that the main chemical facies are Na-Cl, Na-Ca-HCO3, and Na-Cl-HCO3. Silicate weathering control the majority of groundwater samples of the Eocene aquifer, while carbonate dissolution governing the deep groundwater of Eocene carbonate aquifer. Isotope ratios of oxygen (O-18) and hydrogen (H-2) were used to identify the recharge sources, which showed relatively depleted O-18 and H-2 isotopic ratios and relative mixing of groundwater from the Eocene Limestone with paleowaters from the deep Nubian aquifer and water from the Nile River. However, the mixing ratio depends mainly on the distance from the Nile River, depth to groundwater, and local geologic structures also contribute to the mixing pattern. The present study indicates the need for a detailed structural study to detect the locations and properties of fractures as it plays a vital role in feeding the Eocene aquifer from the underlying aquifer. Integration of hydrogeochemical data and isotopic compositions provide a better understanding of the geochemical processes that control the groundwater hydrochemistry of the Eocene carbonate aquifer west of El-Minia, Egypt and in areas with similar conditions.