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 (NEE_c) 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 NEE_c 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 NEE_c 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.