Eutrophic estuaries are hotspots of greenhouse-gas emission, playing a disproportional role in regulating the CO₂, CH₄ and N₂O concentrations in the atmosphere. Numerous studies have shown huge spatial-seasonal variations in the distribution and flux of the three major greenhouse gases, however, the combined greenhouse effect and whether CO₂, CH₄ and N₂O follow similar spatial-temporal variation patterns remain unclear. We measured the distribution and air-sea flux of CO₂, CH₄ and N₂O across the salinity gradient covering all four seasons in a heavily human-perturbated estuary, the Jiulong Estuary (JLE). allowing a comprehensive evaluation of the net greenhouse effect.We found that all gases were supersaturated, and their saturation level declined seaward. By comparison, all the gases exhibited remarkable seasonal variation in both their concentrations and fluxes. Total GWP100-weighted flux varied three- to fivefold across different seasons. Annual mean flux was 40.5 mmol CO₂-eq m^-2 d^-1, with CO₂, N₂O and CH₄ contributing 85.4%, 12.5% and 2.1%, respectively. Dark incubations further reveal contrasting effects of microbial activities on the fate of the greenhouse gases: CO₂ production declined with salinity, CH₄ was consumed and N₂O showed net production throughout the estuary. All the three gases covaried with salinity and nutrients, although these relationships partly reflected shared spatial pattern. After accounting for the salinity effects, residual excess CO₂ was positively correlated with temperature, whereas excess CH₄ was associated with temperature and NH₄⁺; no measured environmental variable was statistically correlated with excess N₂O. Collectively, these findings show that the apparent similar spatial distribution pattern do not imply same controls, but instead the three greenhouse gases were regulated by different processes and environmental variables. Spatially and seasonally resolved multi-gas observations are essential to constrain greenhouse-gas emissions from eutrophic estuaries.