Qena area, Upper Egypt has a limited water resources represented by the River Nile, irrigation canals and groundwater resources. The Quaternary groundwater aquifer is the main water source in the study area. Urbanization and agricultural activities in the study area constitute the main pollution sources of groundwater. Pollution sources in the study area include mixing from wastewater and agrochemicals from agricultural activities. Results of hydrochemical analysis of thirty groundwater samples collected from the study area revealed that groundwater sources are polluted by nitrates, phosphates, ammonia and E. Coli bacteria. Groundwater quality in the study area varied from locality to another concerning its suitability for drinking purposes according to the World Health Organization and Egyptian standards. Most of the collected groundwater samples are not suitable for drinking purposes. On the other hand, groundwater is suitable for irrigation purposes with limited restriction. The present study recommended management of pollution sources including application of agrochemicals and controlling the seepage of wastewater from rural areas as well as management of wastewater treatment plants.