The increase of the reclaimed land for agriculture, especially in the Western Desert of Egypt, aims to cope with the increase of the Egyptian population. The western region of Esna is one of the most promising areas where there are remarkable agricultural activities that depend mainly on groundwater. The present study aims at identifying the recharge sources as well as studying the chemical evolution of groundwater in the Quaternary aquifer which represents the main aquifer in the area. Twenty groundwater level measurements and analyses of the concentrations of trace elements and major ions in 23 groundwater samples, a Nile water sample, and an irrigation canal water sample were done in order to determine the sources of groundwater recharge and its chemical evolution. The subsurface sediment succession in some wells shows the impact of a clay lens on the groundwater salinity in the northwestern part of the area. There is also a significant water leakage from an irrigation canal into the subsurface aquifer causing a local rise of groundwater level. A shallow clay lenses cause water logging near a sewage station that discharges wastewater into drains to be used in the irrigation of a man-made tree forest. Contamination of the aquifer has been detected near the sewer station. This study proves that the main recharge source is the Nile system (the Nile and its irrigation-drainage network). The main geochemical evolution processes are: (1) freshening by Nile system waters, (2) cation exchange, and (3) mineral dissolution and precipitation.