The deep aquifers in Jordan contain non-renewable and fossil groundwater and their extraction is quasi a mining process, which ends in the depletion of these resources. Although aquifers in the majority of groundwater basins in Jordan are vertically and horizontally interconnected stratification in different water quality horizons with generally increasing water salinity with the depth is observed. Many officials and planners advocate the extraction of deep salty and brackish water to be desalinated and used in household, industrial, and agricultural uses. In this article, the quality of the groundwater in the different deep aquifers and areas in Jordan is discussed. The results of this study show that the consequences of the deep groundwater exploitation are not restricted to depletion of the deep aquifers but also that the overlying fresh groundwater will, due to vertical and horizontal interconnectedness of the different aquifers, percolate down to replace the extracted deep groundwater. This will cause the down-percolating fresh groundwater to become salinized in the deep saline aquifers, which means that extracting the deep brackish and saline groundwater is not only an emptying process of the deep groundwater but also it is an emptying process of the fresh groundwater overlying them. The results allow to conclude that any extraction of the deep groundwater in areas lying to the north of Ras en Naqab Escarpment will have damaging impacts on the fresh groundwater in the overlying fresh groundwater aquifers. This article strongly advises not to extract the deep brackish and saline groundwater, but to conserve that groundwater as a base supporting the overlying fresh groundwater resources, and that will help in protecting the thermal mineralized water springs used in spas originating from these deep aquifers.