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To describe nutrient and biofilm dynamics in interstitial habitats of riffles (in a downwelling upwelling sequence), oxygen, nitrate, dissolved organic carbon (DOC) contents, bacterial abundances, hydrolytic and deshydrogenasic activities of biofilms were studied for 18 months in two geomorphologically contrasting riffles of a regulated channel of the Rhone river (a 7th-order stream). The first one was located in an section of the channel affected by river bed incision, whereas the other section has only been slightly impacted by river bed incision. During the transit of surface water through river bed sediments, oxygen consumption, DOC immobilization, and nitrate production were observed especially during the warm seasons when biofilm activity was high. Organic matter decomposition by interstitial biofilms may induce nitrate release by mineralization and nitrification. When the oxygen content decreased strongly during summer, exceptional nitrate depletion occurred in the sediments due to denitrification. A comparison with the Maple River, a 3rd-order stream (Hendricks, 1993) highlights that differences were mostly linked to the origin of groundwater, to differences in stream order (high quantities of nutrients), and to local geomorphological characteristics (heterogeneity in fine sediments and total organic matter - TOM - deposition). River bed incision might induce (1) weak biofilm development and activities in the sediment, (2) changes in vertical distribution of bacteria and biofilm activities, (3) marked temporal variations of biofilm activities, and (4) decrease of sediment efficiency in oxygen consumption, DOC immobilization, and nitrate production.