Carbon fluxes in tidal brackish marshes play a critical role in determining coastal wetland carbon sequestration and storage, thus affecting carbon crediting of coastal wetland restoration. In this study, a process-driven wetland biogeochemistry model, Wetland Carbon Assessment Tool DeNitrification-DeComposition was applied to nine brackish marsh sites in Mississippi River (MR) Deltaic Plain to examine the responses of gross primary productivity (GPP), ecosystem respiration (ER), net ecosystem exchange (NEE), and emissions of methane (CH₄) and nitrous oxide (N₂O) to climate change. Simulations of a normal hydrologic year (2013), dry year (2011) and wet year (2021), and a hypothetical sea level rise (SLR) case were conducted as climate change scenarios. These climate change scenarios were determined by the Palmer Drought Severity Index (PDSI) for the Northeast Division of Coastal Louisiana during 2001–2021. Model results showed that GPP, ER, NEE, CH₄, and N₂O vary with site, and these brackish marshes lost carbon (net CO₂ emission) due to large reduction in primary productivity under the climate scenarios, as well as even during the normal hydrologic year. Average cross-site NEE were 148, 140 and 132 g C m⁻² yr⁻¹ in the dry, wet, and normal years (all net loss of wetland C). Under the hypothetical SLR, NEE were reduced by -25% compared to the normal year, but GPP and NPP were declined by -40% and -70%, respectively. These results suggest that climate change induced changes in soil salinity and water table depth will exacerbate carbon loss from tidal brackish marshes.