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The mid Tafna wadi (N-W Algeria) is exposed to several man induced disturbances including urban, industrial, and agricultural effluents, and alteration of the natural flow regime. The recent installation of a reservoir upstream of the study area has strongly modified the flow regime by extending the period of low water level, and this stream section is only occasionally fed by water releases. Investigations on the hyporheos and benthos of this stream have allowed the comparison of densities, taxa richness and diversity, during three hydrological periods (natural high water, low flow and reservoir water releases), with the aim to highlight effects of the reservoir management on downstream hydrosystems. Species richness and abundance of stygobite crustaceans were low in the hyporheos. Surface water Crustaceans represented 53% of the overall fauna, with Cyclopoidae composing 50% of the Crustaceans. The dominance of the Cyclopoidae was also observed in the hyporheos. Daphniidae were more abundant (37%) in the benthic habitat than in the hyporheic zone. The alternation of high and low discharges appeared to affect the hyporheos more than the benthic communities. The stability concept of the hyporheic habitat does not fit with our results showing a great range of spatial (mosaic habitat) and temporal changes according to the flow regime.