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Coastal marshes take up atmospheric CO2 while emitting CO2, CH4, and N2O. This ability to sequester carbon (C) is much greater for wetlands on a per area basis than from most ecosystems, facilitating scientific, political, and economic interest in their value as greenhouse gas sinks. However, the greenhouse gas balance of Gulf of Mexico wetlands is particularly understudied. We describe the net ecosystem exchange (NEEc) of CO2 and CH4 using eddy covariance (EC) in comparison with fluxes of CO2, CH4, and N2O using chambers from brackish and freshwater marshes in Louisiana, USA. From EC, we found that 182 g C m−2 yr−1 was lost through NEEc from the brackish marsh. Of this, 11 g C m−2 yr−1 resulted from net CH4 emissions and the remaining 171 g C m−2 yr−1 resulted from net CO2 emissions. In contrast, −290 g C m2 yr−1 was taken up through NEEc by the freshwater marsh, with 47 g C m−2 yr−1 emitted as CH4 and −337 g C m−2 yr−1 taken up as CO2. From chambers, we discovered that neither site had large fluxes of N2O. Sustained-flux greenhouse gas accounting metrics indicated that both marshes had a positive (warming) radiative balance, with the brackish marsh having a substantially greater warming effect than the freshwater marsh. That net respiratory emissions of CO2 and CH4 as estimated through chamber techniques were 2–4 times different from emissions estimated through EC requires additional understanding of the artifacts created by different spatial and temporal sampling footprints between techniques.