Nitrite is a toxic intermediate compound in the nitrogen (N) cycle. Elevated concentrations of nitrite have been observed in the Seine River, raising questions about its sources and fate. Here, we assess the role of bottom sediments as potential sources or sinks of nitrite along the river continuum. Sediment cores were collected from two depocenters, one located upstream, the other downstream, from the largest wastewater treatment plant (WWTP) servicing the conurbation of Paris. Pore water profiles of oxygen, nitrate, nitrite and ammonium were measured. Ammonium, nitrate and nitrite fluxes across the sediment-water interface (SWI) were determined in separate core incubation experiments. The data were interpreted with a one-dimensional, multi-component reactive transport model, which accounts for the production and consumption of nitrite through nitrification, denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA). In all core incubation experiments, nitrate uptake by the sediments was observed, indicative of high rates of denitrification. In contrast, for both sampling locations, the sediments in cores collected in August 2012 acted as sinks for nitrite, but those collected in October 2013 released nitrite to the overlying water. The model results suggest that the first step of nitrification generated most pore water nitrite at the two locations. While nitrification was also the main pathway consuming nitrite in the sediments upstream of the WWTP, anammox dominated nitrite removal at the downstream site. Sensitivity analyses indicated that the magnitude and direction of the benthic nitrite fluxes most strongly depend on bottom water oxygenation and the deposition flux of labile organic matter.