We investigated the spatiotemporal heterogeneity, source-sink dynamics, and regulatory drivers of nitrous oxide (N₂O) in the subtropical Jiulong River Estuary (JRE) through integrated field surveys and in situ incubations. Dissolved N₂O concentrations ranged from 6.1 to 185.4 nmol·L^-1, exhibiting a pronounced decline along the salinity gradient from freshwater-dominated upstream to marine-influenced downstream regions. The release of N₂O from the sediment-water interface through processes such as Submarine Groundwater Discharge (SGD) and pore water exchange (PEX) constitutes a significant source of N₂O in the JRE, whereas microenvironments associated with suspended particulate matter (SPM) accounted for 73.8% of net N₂O consumption for water column in the upper-middle estuary. Hydrologically, tidal cycles and river plume mixing drive short-term spatial variability, while salinity serves as the overarching long-term regulator of N₂O distribution. Notably, integrated basin–coastal management over the past decade has reduced area-weighted N₂O emission fluxes by more than 70%. These findings provide a mechanistic foundation for evidence-based greenhouse gas mitigation strategies and highlight the efficacy of coordinated management in subtropical estuarine ecosystems.