Given the complex source composition, spatiotemporally variable transport and transformation processes, and the difficulty of accurate nitrate source identification in river–coastal interaction zones influenced by both terrestrial inputs and tidal mixing, this study developed an integrated source-tracking framework combining flux monitoring, isotope-based apportionment, and numerical simulation for a typical river network–estuary system in the Pearl River region. This framework quantitatively resolved the composition of nitrate pollution sources and elucidated the variation in transport pathways and the dynamic response mechanisms of nitrate pollution under the complex hydrodynamic conditions of river–sea interactions. The results showed that nitrate inputs in the study area were primarily derived from agricultural non-point sources (51.4%) and domestic sewage (20.4%). This overall pattern was broadly consistent across terrestrial input boundaries, with substantial spatial heterogeneity. Tidal oscillation and blocking effects enhanced pollutant mixing and redistribution within the river network–estuary system, thereby homogenizing the spatial distribution of nitrate concentrations across coastal transects. Scenario simulations revealed that changes in nitrate concentrations in runoff induced a linear response in pollution loads, while exerting only a limited effect on source composition. In contrast, variations in hydrodynamic conditions generated a systematic asymmetric response, substantially altering the relative contributions of pollution sources at different regions through coupled changes in pollutant transport fluxes and tidal intrusion intensity.Overall, the nitrate source structure in the interaction zone is determined not only by terrestrial inputs but also by the coupled effects of runoff and tides. The integration of flux monitoring, isotope source apportionment, and numerical modeling effectively improves both the accuracy and spatial resolution of nitrate source identification in river–coastal interaction zones, providing a scientific basis for coordinated land–sea environmental management and targeted regional pollution control.