The El Minia governorate lies within the Nile Valley, surrounded by calcareous plateaus to the east and west. The present study focuses on the hydrogeochemistry of the Eocene limestone aquifer at some wadis in the east El Minia governorate, Eastern Desert, Egypt. Hydrogeologically, two main aquifers are encountered in the study area, namely the Maghagha marly limestone and the Samalut chalky limestone aquifers. The Maghagha aquifer is composed of alternating layers of marly limestone and shale with thicknesses ranging from 3.49 m to 177.05 m and a groundwater depth ranging from 8.5 m to 59.27 m which reflects low groundwater potentiality. The groundwater salinity representing this aquifer ranges from 603.5 mg/L to 978.5 mg/L, reflecting fresh water type. Samalut aquifer is made up of chalky, cavernous and fractured limestone with thickness ranging from 30 m to 205 m and groundwater depth ranging from 9 m to 86.77 m, which indicates good groundwater potential. The groundwater salinity of the concerned aquifer ranges from 349.7 mg/L to 2043.9 mg/L, reflecting fresh to possibly brackish water types. Groundwater in the study area is of meteoric water origin; recent recharge is mainly controlled through the presence of fractures and their densities. The majority of groundwater samples in the study area are suitable for drinking and irrigation purposes.