The depletion of aquifer systems in arid and semiarid regions worldwide is causing acute water scarcity and quality degradation, and leading to extensive ecosystem damages. Groundwater is exposed to a variety of anthropic water pollution as raw wastewater disposal in the Draa wadi and the use of septic tanks. In this respect a study performed in some wells of Fezouata (South-east of Morocco), aimed at both discovering the main components of the aquatic subterranean fauna unknown up to now in this area, and the potential relationships between this fauna and the water quality The principal physico-chemical characteristics of water were measured between November 2019 to March 2021 for 15 wells which selected considering their position with respect to the pollution sources known in surface. The Fezouata groundwater is distinguished by its high salinity. with an increasing gradient from upstream to downstream. The aquatic fauna in the 15 wells showed 12 stygofauna species. In the protected wells which are situated far from the pollution sources, the fauna is dominated by the Amphipods Metacrangonctydae, Stenasellidae, Cirolanidae, Thermosbaenacea and Gastropods. On the other hand, in the less protected well, close to the pollution sources, the fauna is made of epigean species such as insect’s larva mainly Culicidae and Chironomidae. The analysis of the water quality and the subterranean biodiversity shows that the latter decreases with increasing groundwater pollution. It seems that the impact of the acute pollution affected the stygocenose even by reducing drastically the biodiversity.