The potential for carbon sequestration in coastal wetlands is high due to protection of carbon (C) in flooded soils. However, excessive flooding can result in the conversion of the vegetated wetland to open water. This transition results in the loss of wetland habitat in addition to the potential loss of soil carbon. Thus, in areas experiencing rapid wetland submergence, such as the Mississippi River Delta, coastal wetlands could become a significant source of carbon emissions if land loss is not mitigated. To accurately assess the capacity of wetlands to store (or emit) carbon in dynamic environments, it is critical to understand the fate of soil carbon following the transition from vegetated wetland to open water. We developed a simple soil carbon model representing soil depths to 1 m using the data collected from a Louisiana coastal salt marsh in the Mississippi River Deltaic Plain to predict soil carbon density and stock following the transition from a vegetated salt marsh to an open water pond. While immediate effects of ponding on the distribution of carbon within the 1-m soil profile were apparent, there were no effects of ponding on the overall, integrated, carbon stocks 14 years, following wetland submergence. Rather, the model predicts that soil carbon losses in the first meter will be realized over long periods of time (∼200 years) due to changes in the source of carbon (biomass vs. mineral sediment) with minimal losses through mineralization.