Intertidal marshes serve as important storm buffers, wildlife habitat, and a source of economic value. Central to coastal biogeochemical processes, they play a disproportionately large role in the global carbon cycle. These systems are experiencing large-scale land loss due to sea level rise, land use change, and human alteration of coastal rivers, with some of the highest rates observed along the Gulf Coast. High primary productivity and low oxygen soils enable long-term sequestration of atmospheric carbon, defining them as blue carbon ecosystems. However, anaerobic respiration in the sediment can release methane (CH4), remineralizing a portion of this stored carbon. Due to a high global warming potential, CH4 emissions can offset the cooling effect of CO2 uptake, particularly over the short-term, making the balance between these fluxes critical to a marsh’s net radiative impact. In saline environments, sulfate reducers typically outcompete methanogens, suppressing CH4 emissions in salt marshes. Yet, recent studies suggest that methanogens can coexist with sulfate reducers, with vegetative substrate potentially influencing this dynamic. In coastal Mississippi, the Pascagoula River estuary – fed by the largest undammed river by volume in the contiguous United States – and the Grand Bay estuary – cut off entirely from its founding river – lie less than 10 miles apart but demonstrate contrasting hydrological regimes. Using long-term, seasonal deployments of automatic flux chambers at these sites, we present the first known analysis of both carbon dioxide and methane vertical flux in coastal Mississippi. Here, we contrast measured fluxes across sites and vegetative cover to evaluate the drivers of greenhouse gas exchange in Mississippi coastal marshes. These findings inform how vegetation and hydrology shape greenhouse gas dynamics, informing assessments of land loss, restoration, and management in Gulf Coast marshes.