Methane (CH₄) is steadily increasing in the atmosphere from different sources including wetlands. However, there is limited landscape level CH₄ flux data in deltaic coastal systems where the availability of freshwater is impacted by the combined effect of climate change and anthropogenic impacts. Here we determine potential CH₄ fluxes in oligohaline wetlands and benthic sediments in the Mississippi River Delta Plain (MRDP), which is undergoing the highest rate of wetland loss and most extensive hydrological wetland restoration in North America. We evaluate potential CH₄ fluxes in two contrasting deltaic systems, one undergoing sediment accretion as result of a freshwater and sediment diversions (Wax Lake Delta, WLD), and one experiencing net land loss (Barataria-Lake Cataouatche, BLC). Short- (<4 days) and long-term (36 days) incubations using soil and sediment intact cores and slurries were performed at different temperatures representing seasonal differences (10, 20, 30 °C). Our study revealed that all habitats were net sources of atmospheric CH₄ in all seasons, and CH₄ fluxes were generally the highest for the 20 °C incubation. The CH₄ flux was higher in the marsh habitat of the recently formed delta system (WLD) with total carbon content of 5–24 mg C cm⁻³ compared to the marsh habitat in BLC, which had high soil carbon content of 67–213 mg C cm⁻³. This suggests that the quantity of soil organic matter might not be a determining factor in CH₄ flux. Overall, benthic habitats were found to have the lowest CH₄ fluxes indicating that projected future conversions of marshes to open water in this region will impact the total wetland CH₄ emission, although the overall contribution of such conversions to the regional and global carbon budgets is still unknown. Further research is needed to expand the CH₄ flux studies by simultaneously using several methods across different wetland habitats.