Within Algerian Sahara, the Oued M'ya basin contains four major superposed aquifers that exhibit water upwelling phenomena and form wetland and sabkha environments. These events raise the likelihood of environmental degradation in urban and agricultural areas. This research aims to better understand the origins and dynamics of this complex issue. It is a structural approach to investigating the causes of the physicochemical and geochemical quality of the surface and groundwater in this zone and their relationship to the aforementioned phenomena. The effects of hydro-structural features such as lineaments and fractures on the occurrence and quality of surface and groundwater are studied. In addition, plans and practical methods for managing water upwelling are suggested. GIS and statistical tools were used to apply manual and automatic recognition techniques. The automatic method was used to statistically analyze lineaments and their presentation. These techniques enabled us to determine the parameters of the lineament, such as its direction, length, and frequency. The lineament map was created by examining satellite images of the area and identifying several families of lineaments based on preferential and global orientations. By comparing surface and subsurface data, we could better understand the regional and local hydrogeological implications of lineaments and their regional geological context. As a result, the nature of subsurface lineaments was evaluated and confirmed. The piezometric map and the location of geochemical anomalies show that faults and associated fractures significantly impact groundwater movement. Faults can either facilitate or impede groundwater flow depending on their location in the study area and whether they are driven by tension, compression, or shear stresses. The nature of the material involved, the degree of deformation induced, the materials present in the fault system, and the depth beneath the surface all influence the role of faults as preferred pathways or barriers to groundwater flow. Faults can also contribute to the formation of surface water in arid zones by forming depressions or basins that collect water and form wetlands, such as Sebkhas and Chotts. Lineaments and faults can allow freshly or slightly less salted groundwater to reach the surface and mix with salty surface water, resulting in varying brininess and water chemistry in different wetland regions. Fractures can affect the water chemistry of these wetland ecosystems by controlling the water supply and the degree of mixing between groundwater and saline surface water. The identified geochemical abnormalities (mixing zones) can be linked to various factors, including the flow rate, origin, and path of the recharge zones and the structural framework and rock properties of subsurface reservoirs. According to previous research, this local study's findings can be extrapolated to the regional scale of the Saharan platform. Several faults influence the latitudinal limit of the Continental Intercalaire (CI) aquifers, according to the structural analysis of the studied area. At the local and regional scales, groundwater geochemistry and mineralogy revealed a clear spatial correlation between hydrogeochemical facies clusters and reservoir compartments.