According to the chemical composition of water, a vertical hydrochemical stratification has been observed, sodium bicarbonate water is predominant in deep Nubian aquifer, while calcium bicarbonates occur in the marginal and shallower zones of this aquifer. In comparison with more arid regions of North Africa no chloride types has been found within it. Stable isotope data clarifies the interaction between the different water bodies. The Nubia water is the most depleted on its stable heavy isotopes content while surface water is very enriched due to evaporation. The results give very important information about the sources of recharge of the groundwater in the area. The groundwater is mainly meteoric water from two sources of recharge first is paleo-water of paleo-climatic and second is recent water of local precipitation.