In this paper, the water resources system in Qena governorate was proposed by studying the natural and hydrogeological conditions of the governorate, including its location, groundwater, climate and rain. Also Studying the Social and economic conditions of the study area including its population, crops, drinking water and etc. Through the water balance model and a Water Shortage Quality Index on 3 scenarios: the base case scenario in 2018, the realistic scenario in 2050 without any adaptation measures and the optimistic scenario in 2050, which considers adaptation measures of water shortage.