Groundwater in the Saïss Basin is a resource of economic and social importance for the region. They are also the reservoir of an original biological diversity. In this context, the objective of this study is to contribute to a wider knowledge of the underground aquatic fauna in Morocco and to evaluate the effect of anthropic pressure on the quality of groundwater and on the aquatic fauna; thus increasing the vulnerability of stygobies living in these underground aquatic ecosystems. The biotypological study showed that the overall faunal richness of the stations decreases and that the stygobian fauna is the most sensitive to pollution, decreasing first and disappearing completely in case of a major pollution. These results represent an important contribution to the regional biodiversity and can be influenced mainly by local factors, in particular the levels of protection of these underground ecosystems.