AbstractEstuaries are key areas for terrestrial material transport and marine biogeochemical processes, particularly those of dissolved inorganic nitrogen (DIN) and dissolved organic nitrogen (DON). However, the fate of DON in estuaries with a high runoff remains poorly understood. In this study, we explored the translocation and transformation of DON in the Pearl River Estuary (PRE) and adjacent coastal areas of southern China based on DON concentrations, optical and fluorescence characteristics, and environmental parameters. The results revealed that DIN and DON exhibited dissimilar distributions. The distribution of DIN was primarily influenced by freshwater‐seawater mixing. In contrast, biological processes and freshwater‐seawater mixing shaped the distribution of DON. High levels of DON in the terrestrial‐dominated zone were predominantly anthropogenic sources through terrestrial inputs, whereas DON in the freshwater‐seawater mixing zone and seawater‐based zone were mainly influenced by biological activities, as high concentrations of Chla were observed in these two areas. DON exhibits fast dilution in low‐salinity areas and retention in moderate‐salinity areas (freshwater‐seawater mixing area) in summer and winter, while undergoes a rapid decrease in open water areas during winter. Consequently, DON in the PRE and adjacent coastal areas exhibited nonconservative mixing despite seasonal variations. These findings provide novel insights into the role of DON in nitrogen biogeochemical processes in river‐dominated estuaries and adjacent coastal areas.