The biodiversity and quality of subterranean waters were comparatively studied in the Tarf plain near Oum-El-Bouaghi and in the Ksar S’bahi in Oum-El-Bouaghi, in North-eastern Algeria. For this purpose, physicochemical and faunistic analyses were carried out on the water of ten stations located in the area of Tarf, and thirteen in the area of S’bahi. In the wells of Tarf, the average stygobiologic diversity was relatively high in the wells located upstream the dumping site from the city where the groundwater presented low contents of nitrates and orthophosphates. In contrast, the wells located in the spreading zone of Tarf wastewaters were characterized by the scarcity or the absence of stygobic species; in these latter wells, the water was highly polluted. It was rich in nitrates, nitrites, ammonium, and the conductivity was rather high. In the area of S’bahi, the faunistic inventory recorded ten species, some of which were living in hot springs. The subterranean water was highly mineralized. In the two studied areas, biodiversity decreased when well water was locally polluted.