We conducted a study to address uncertainties associated with the metabolism and net carbon fluxes for the tidal wetland and estuarine portion of the coastal ocean because of these zones disproportionately large role in ocean carbon dynamics. We measured open water diurnal O2 and CO2 dynamics seasonally in the Duplin River salt marsh-estuary in Georgia, USA with a particular focus on the marsh-estuary linkage associated with tidal flooding. We observed that the overall system was a net source of CO2 to the atmosphere and adjacent coastal ocean and a net sink for oceanic and atmospheric O2. Rates of metabolism were extremely high, with respiration (R: 43 mol/m2/yr) exceeding gross primary production (GPP: 28 mol/m2/yr). Rates of metabolism measured with CO2 were substantially higher than with O2. The net heterotrophy of the aquatic salt marsh-estuary system is supported primarily by the net production of the salt marsh proper.