The land-to-ocean export of terrestrial organic carbon is a key process regulating the global carbon cycle. Estuaries serve as critical interfaces through which riverine organic carbon must pass before reaching the coastal ocean. Within these environments, strong physicochemical gradients can substantially alter the composition and fate of terrestrial organic matter. However, the extent to which terrestrial organic carbon is transformed under different hydrological conditions, and whether different organic matter components exhibit distinct transport and transformation behaviors, remains poorly understood. To address these questions, we collected water samples along the salinity gradient of the Jiulong Estuary during four seasons. We quantified lignin phenols and dissolved black carbon (DBC) and characterized dissolved organic matter (DOM) molecular composition using FT-ICR-MS. Our results show that the estuarine behavior of terrestrial DOM is strongly linked to its molecular character. Highly aromatic compounds, such as DBC, were relatively resistant to biodegradation and therefore exhibited near-conservative behavior over the estuarine flushing time. In contrast, less aromatic terrestrial organic matter was more susceptible to microbial degradation and displayed clear removal along the salinity gradient. These findings demonstrate that different terrestrial organic matter fractions undergo distinct transport and transformation processes during estuarine transit. Such differential behavior should be considered when addressing the riverine organic matter that eventually exported to the coastal seas and its implications for the global carbon cycle.