Around the world, groundwater supply is critical for vital needs such as drinking and irrigation. This work investigates groundwater in the carbonate aquifer of the Middle Miocene in the east El Minia area, Egypt. In this regard, thirty-two groundwater samples were collected. The water samples were analyzed for Ca2+, Mg2+, Na+, K+, Cl−, SO42−, NO3−, CO2−, HCO3−, Fe, Mn, Cd, As, Cr, Cu, and Pb. Groundwater has been evaluated using two methods, which are water quality index (WQI) and health risk assessment (HRA). The predominant groundwater is soft water, and the samples range in salinity from fresh to slightly salty. The groundwater mostly falls into the alkaline water type. All the groundwater samples under study are deemed low quality for human consumption due to water contamination. Fe, Mn, Cd, Cu, and Pb have high HQnc values, which can result in non-carcinogenic health issues in adults, while Mn, Cu, and Pb can give rise to non-carcinogenic health issues in children.