The dynamics of the water exchanges between surface and subsurface are expected to playan important role in the self purification capacities of streams with a porous bottom. The tested hypotheses are(i) that downwelling surface water increased the storage of organic pollution in the hyporheic layer ("storageeffect") and (ii) conversely, that upwelling groundwater had a beneficial effect on the ecological quality andthe rehabilitation capacity of the stream. From a site experiment, downwellings of surface water andupwellings of hyporheic water are described both by hydrological dynamic indices, water chemical measuresand active exchange indicator species of oligochaetes. Results confirm these functional hypotheses and helpto define first rules for managing the ecological quality of this type of streams.