Large, river‐dominated estuaries provide important land‐ocean interfaces for biogenic element fluxes that impact global marine biogeochemistry. However, the reactivity and fate of dissolved organic matter (DOM) in this dynamic region remain not well understood. In this study, three cruises were conducted in February, May, and July 2017 in the Changjiang Estuary and adjacent sea (CEAS). Incubation experiments to determine photochemically and/or biologically mediated degradation of terrigenous and marine DOM were performed. Dissolved organic carbon (DOC), chromophoric DOM (CDOM) absorption, and total dissolved amino acids (TDAAs) were measured. DOM photodegradation and transformation were indicated by the CDOM spectral slope (S275−295) and diagenetic state by DOC‐normalized yields of TDAA [TDAA (%DOC)]. From the river to the open sea, DOC showed non‐conservative mixing and was rapidly removed in low salinity areas. Photodegradation, biodegradation, and photoenhanced biodegradation are important DOC removal mechanisms and exhibit specific responses depending on DOC source and composition. Terrigenous DOM is vulnerable to photodegradation, while marine DOM experiences rapid biodegradation. Contrary to DOC, TDAA (%DOC) increased from the river to the nearshore and then decreased toward the open sea, indicating the contribution of fresh marine plankton production. A box model showed that the annual DOC removal of CEAS was 2.6 ± 1.9 × 106 tons. Seaward increase of ammonium (NH4‐N) was observed in the CEAS; photoammonification, biomineralization of autochthonous and allochthonous DOM are potential NH4‐N regeneration mechanisms. A model was developed to calculate surface DOC concentrations based on CDOM absorption coefficients allowing high‐resolution monitoring of DOC in the CEAS.