The Southern Algerian Aquifer System comprises two main deep aquifer layers: the Continental Intercalary Formation and the Terminal Complex Formation. These aquifer layers cover an area of more than 700,000 km2 in Algeria. Due to desert-like climatic conditions, these formations are poorly recharged, with approximately 1 billion cubic meters (BCM) of water infiltrating annually, mainly in the mountainous regions of the Saharan Atlas. The Saharan Aquifer System is exploited through over 6500 water points, including boreholes and springs in the Continental Intercalary and Terminal Complex formations. Over the past two decades, there has been an exponential growth in the number of boreholes and the frequency of their use, now reaching 1.33 BCM per year. If this trend continues, it could raise serious concerns about the future of Saharan regions, where the initial signs of declining water availability are already evident. The rapid expansion of exploitation of the southern Algerian aquifers has fundamentally altered the perception of this activity. However, this expansion faces several significant risks associated with its development, including water salinization, loss of artesian pressure, depletion of outlets, and excessive pumping levels. Therefore, sustainable management of this vital resource is imperative, incorporating appropriate management practices and implementing regulations to prevent overexploitation and adverse impacts on the aquifer ecosystem. Despite the limited recharge, the scale and the aquifer thickness have led to the accumulation of considerable water reserves. This chapter aims to comprehensively investigate the methods employed for groundwater utilization in southern Algeria, with a dual focus on elucidating existing issues and confronting contemporary challenges. It aims to examine approaches for enhancing and rationalizing the extraction of water from Saharan aquifers to promote regional advancement, all the while prioritizing the preservation of long-term sustainability.