The desert regions are suffering from the scarcity of precipitation and hence experience deficiency of reliable fresh water resources. Groundwater is the main source of water supply. Nevertheless, it is finite and should be managed carefully. The new technologies of groundwater management must be applied on desert regions. The decision-makers should be aware of the early signals of potential hazards and available resources in order to anticipate endangered areas. In this monograph the hydrogeology of arid basins is explained in detail and potential management concepts and tools is applied. El-Qaa basin has thick Quaternary aquifer that is hosting paleowater and is receiving indirect recent recharge from eastern high mountainous terrain. The present exploitation rate exceeds recharge and captures only about 30% of recharge and will cause severe draw down. To optimize exploitation and long-term protection of the aquifer, redistribution of exploitation is proposed. Redistribution is devoted for capturing ground water outflow and preventing salt-water intrusion.