Riverine ecosystems receive nitrogen loads from point and diffuse sources that are transferred downstream. Such loads may undergo poorly explored retention and dissipation processes, varying along gradients of nitrogen availability due to different interactions among primary producers and microbial communities. We measured carbon uptake and nitrogen fluxes in microcosms containing riverine sediments with benthic algae and submerged macrophytes (Vallisneria spiralis L.). Coupled nitrification–denitrification rates were determined via 15N–NH4+ injection in the pore water and quantification of the produced 29N2 and 30N2. Two sites with different N–NO3- concentration and sediment organic content were investigated. We hypothesized that: (1) N–NO3- availability promotes water column N uptake and attenuates primary producers-bacteria competition; (2) coupled nitrification– denitrification is stimulated by radial oxygen loss from roots; (3) macrophyte meadows favour both temporary nitrogen retention and permanent removal. Sediments with V. spiralis were mostly inorganic C and N sinks and always displayed higher coupled nitrification–denitrification rates compared to sediments with microphytobenthos. Highest rates, up to 100 lmol N m-2 h-1, were measured at the more eutrophic site and in the light. This is likely due to a shift from root to leaf uptake at the N–NO3 - rich site, attenuating plant-bacteria competition, and to increased radial oxygen loss in organic-rich sediments, stimulating nitrification. High rates of N uptake and loss in lotic sediments represent natural buffers preventing N transport downstream and stress the need to preserve aquatic vegetation and its ecosystem services.