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Nitrogen dynamics were studied in the interstitial environment (i.e. hyporheic zone) of a sandy-bottom stream in a rural landscape. A third-order stream in Brittany (France) was studied at 11 stations (riffles) to evaluate spatial patterns of water exchange between surface and interstitial habitats. More intensive sampling was conducted in three riffles selected according to their hydrological characteristics. Chemical characteristics (especially nitrogen) and microbial denitrification were studied at 12.5 and 25 cm depth upstream, and 25 cm depth downstream of each riffle. This study confirms that the interstitial habitat of a N-rich stream acts as a sink for the nitrate-nitrogen. Experimental manipulation of sediment cores indicates that denitrification is limited by carbon in surface (i.e. benthic) and by nitrate in hyporheic sediments. River regulation increases inputs of fine sediments, modifies river channel location, and generates changes in the spatial patterns of biogeochemical processes, water origins, and hydrologic exchanges. Copyright (C) 2004 John Wiley Sons, Ltd.