Discharge modulates nitrogen removal capacity through coupled physical and biogeochemical forcing in a river-dominated estuary

River-dominated estuaries attenuate terrestrial nitrogen loading and act as critical filters between land and ocean, yet how discharge regulates system-scale nitrogen removal remains poorly resolved. Here, we combined field observations with an extended coupled hydrodynamic–water quality model to investigate nitrogen removal in the Pearl River Estuary (PRE). The model represents water–sediment interactions, incorporates a thermodynamically ordered sediment redox cascade, and resolves multiple nitrogen removal pathways. Simulations for a low-flow year (2021) and a high-flow year (2022), together with a 2 × 2 factorial forcing experiment, revealed a pronounced decoupling between nitrogen loading and removal efficiency: inputs increased from 313.8 to 748.8 kt and exports from 129.8 to 498.8 kt, whereas biogeochemical loss increased only from 80.2 to 93.5 kt, reducing removal efficiency from 25.5% to 12.5%. This decoupling arose because elevated discharge jointly altered physical transport and the assimilative pathway of primary production, increasing direct seaward export while reducing labile particulate organic nitrogen delivery to sediment and weakening internal nitrogen attenuation. These results highlight the need for integrated, process-based evaluation of estuarine nitrogen removal across seasons and years to better inform nutrient management under variable hydrological conditions.