Many groundwater and surface water bodies around the world show a puzzling and often steady increase in nitrogen (N) concentrations, despite a significant decline of agricultural N inputs. This study uses a combination of long-term hydrogeochemical and hydraulic monitoring, molecular characterization of dissolved organic matter (DOM), column experiment, and reactive transport modeling to unravel the processes controlling N-reactive transport and mass budgets under the impacts of dynamic hydrologic conditions at a field site in the central Yangtze River Basin. Our analysis shows that the desorption of ammonium (NH4+) from sediments via cation exchange reactions dominates N mobilization and aqueous N concentrations, while the mineralization of organic N compounds plays only a minor role. The reactive transport modeling results illustrate the important role of cation exchange reactions that are induced by temporary NH4+ input and cation concentration changes under the impact of both seasonal and long-term hydrologic variations. Historically, cation exchangers have acted as efficient storage devices and mitigated the impacts of high levels of NH4+ input. The NH4+ residing on cation exchanger sites later acts as a long-term N source to waters with the delayed desorption of sediment-bound NH4+ induced by the change of hydrologic conditions. Our results highlight the complex linkages between highly variable hydrologic conditions and NH4+ partitioning in near-surface, river-derived sediments.