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Benthic and hyporheic (i.e. the water-saturated interstitial zone beneath river bed-sediments) processes together modify particulate and dissolved nutrient fluxes in streams, but the relative importance of these processes remains unstudied in large rivers. Changes in material and nutrient fluxes (total suspended matter, biodegradable and refractory dissolved organic carbon, and nitrate) were monitored along a reach with a regulated discharge (a by-passed section downstream of a dam). Mass balance diagrams highlight a contrasting functioning between upstream and downstream parts of this sector of the Rhone River (Pierre-Benite sector, France). At the upstream location close to the water input, characterized by partially clogged sediments and large lentic zones, decrease in total suspended matter (TSM) and biodegradable dissolved organic carbon (BDOC) fluxes resulted from high rates of benthic processes (i.e. sedimentation, respiration and mineralisation). At the downstream location, characterized by strong vertical water exchanges in a large riffle, nutrient changes resulted from the combination of processes that took place at the surface of the stream bed and during water percolation through riffle sediments. Physical benthic processes (scouring of periphyton, erosion and resuspension of sediment due to higher surface velocity) lead to an increase of TSM and DOC fluxes. Within the riffle, decomposition and mineralisation of organic matter in the first meter of the infiltration zone, and physical entrapment of RDOC, make the riffle as a sink for DOC and a source of nitrate. The significant contribution of the riffle to the self-purification capacities of this large river reach shows the relevance of including interstitial compartment in self-purification studies.