Estuaries are an important source of greenhouse gases to the atmosphere, but uncertainties remain in the flux rates and production pathways of greenhouse gases in these dynamic systems. This study performs simultaneous high resolution measurements of the three major greenhouse gases (carbon dioxide, methane, and nitrous oxide) as well as carbon stable isotope ratios of carbon dioxide and methane, above and below the pycnocline along a salt wedge estuary (Yarra River estuary, Australia). We identified distinct zones of elevated greenhouse gas concentrations. At the tip of salt wedge, average CO2 and N2O concentrations were approximately five and three times higher than in the saline mouth of the estuary. In anaerobic bottom waters, the natural tracer radon (222Rn) revealed that porewater exchange was the likely source of the highest methane concentrations (up to 1302 nM). Isotopic analysis of CH4 showed a dominance of acetoclastic production in fresh surface waters and hydrogenotrophic production occurring in the saline bottom waters. The atmospheric flux of methane (in CO2 equivalent units) was a major (35-53%) contributor of atmospheric radiative forcing from the estuary, while N2O contributed <2%. We hypothesize that the release of bottom water gases when stratification episodically breaks down will release large pulses of greenhouse gases to the atmosphere.