Estuaries are important atmospheric sources of methane (CH₄) and nitrous oxide (N₂O), yet gas dynamics in barrage-regulated estuaries remain poorly understood. In this study, we investigated the dynamics of CH₄ and N₂O in the Nakdong River estuary, Korea, where barrage construction has substantially altered freshwater–seawater exchange. Six field surveys were conducted to capture the spatial and seasonal variability of CH₄ and N₂O in relation to barrage operation. Dissolved CH₄ and N₂O concentrations ranged from 22 to 872 nM and 19 to 409 nM, respectively, with CH₄ peaking in June and remaining relatively uniform otherwise, whereas N₂O reached its lowest levels in September with relatively consistent values during the remaining periods. This seasonality is likely associated with high water temperature, which enhanced microbial gas production, and increased freshwater discharge through barrage opening during the summer monsoon, driving the June CH₄ maximum, whereas the September N₂O minimum likely resulted from enhanced denitrification, as evidenced by the increased bacterial population. Atmospheric CH₄ and N₂O fluxes ranged from 37 to 675 and 20 to 619 μmol m⁻² d⁻¹, respectively, falling within the range reported for estuaries worldwide, with the flux variability primarily controlled by concentrations and wind-driven gas transfer velocity. During periods of high summer discharge, barrage gate opening enhanced the transport of CH₄ and N₂O to the coastal ocean, indicating that barrage opening shifts gas export from atmospheric emission toward downstream transport, where the gases are more likely to be removed via oxidation than to be emitted to the atmosphere. Overall, this study demonstrates that barrage operation is a key control on the balance between atmospheric emission and downstream export of greenhouse gases in barrage-regulated estuarine systems, providing a basis for future assessments and long-term monitoring of greenhouse gas dynamics in similarly modified estuaries.