Wetland ecosystems hold nearly a third of the global soil carbon pool, but as wetlands rapidly disappear the fate of this stored soil carbon is unclear. The aim of this study was to quantify and then link potential rates of microbial decomposition after vertical drowning of vegetated tidal marshes in coastal Louisiana to known drivers of anaerobic decomposition altered by vegetation loss. Profiles of potential CH₄ and CO₂ production (surface to 60 cm deep) were measured during anaerobic incubations, organic matter chemistry was assessed with infrared spectroscopy, and soil porewater nutrients and redox potentials were measured in the field along a chronosequence of wetland loss. After vertical drowning, pond soils had lower redox potentials, higher pH values, lower soil carbon and nitrogen concentrations, lower lignin: polysaccharide ratios, more NH₄⁺ and PO₄³⁻, and higher rates of potential CO₂ release than vegetated marsh soils. Potential CH₄ production was similar in vegetated marshes and open water ponds, with depth-dependent decreases in CH₄ production as soil carbon concentrations increased. In these anoxic soils, vegetation loss exerts a primary control on decomposition rates because flooding drives sustained increases in porewater nutrient availability (NH₄⁺ and PO₄³, dissolved organic carbon) and decreases in redox potential (from −150 to −500 mV) that lead to higher potential CO₂ fluxes within a few years. Without new carbon inputs following wetland loss, the sustained decomposition in open water ponds may lead to losses of stored soil carbon and could influence global carbon budgets.