The fluvial nitrogen dynamics at locations around weirs are still rarely studied in detail. Eulerian data, often used by conventional river monitoring and modelling approaches, lags the spatial resolution for an unambiguous representation. With the aim to address this knowledge gap, the present study applies a coupled 1D hydrodynamic–water quality model to a 26.9 km stretch of an upland river. Tailored simulations were performed for river sections with water retention and free-flow conditions to quantify the weirs’ influences on nitrogen dynamics. The water quality data were sampled with Eulerian and Lagrangian strategies. Despite the limitations in terms of required spatial discretization and simulation time, refined model calibrations with high spatiotemporal resolution corroborated the high ammonification rates (0.015 d−1) on river sections without weirs and high nitrification rates (0.17 d−1 ammonium to nitrate, 0.78 d−1 nitrate to nitrite) on river sections with weirs. Additionally, using estimations of denitrification based on typical values for riverbed sediment as a reference, we could demonstrate that in our case study, weirs can improve denitrification substantially. The produced backwater lengths can induce a means of additional nitrogen removal of 0.2-ton d−1 (10.9%) during warm and low-flow periods.