Coastal wetlands protect coastlines through efficient storage of organic carbon (OC) that decreases wetland vulnerability to sea level rise (SLR). Accelerated SLR is driving saltwater intrusion and altering vegetation communities and biogeochemical conditions in coastal wetlands with uncertain implications. We quantified changes in OC stocks and fluxes driven by 1) saltwater and phosphorous intrusion on freshwater and brackish marshes, 2) vegetation along an experimental saltmarsh to mangrove gradient, 3) saltwater intrusion and vegetation change across a marsh to mangrove ecotone, and 4) vegetation change and mangrove forest development along a marsh to mangrove ecotone. Increasing salinity in freshwater marshes decreased root biomass and soil elevation within one year. In brackish marshes, increased salinity decreased root productivity and biomass and increased root breakdown rate (k), while added salinity did not increase elevation loss. In our experimental marsh-mangrove ecotone, mangrove vegetation promoted higher organic carbon (OC) storage by increasing above and belowground biomass and reducing organic matter k. However, mangroves also increased belowground k, and decreased allochthonous marine subsidies, indicating the potential for OC storage trade-offs. In the Southeast Everglades, we identified strong interior-coastal gradients in soil stoichiometry and mangrove cover. Interior freshwater soil conditions increased k, while total soil OC stocks decreased toward the coast indicating that saltwater intrusion is driving large scale soil OC loss. In the southeast Everglades, mangrove expansion increased root biomass and root productivity, but did not mitigate the overall loss of OC stocks toward the coast. Similarly, in the southwest Everglades, saltwater intrusion drove a decrease in soil OC. However, mangrove encroachment drove a rapid recovery and increased OC stocks. Mangrove encroachment doubled aboveground biomass within the last ten years, increased it 30 times in the last 30 years, and doubled belowground biomass after 20 years. Our research shows that 1) moderate saltwater intrusion without mangrove encroachment will lead to a loss in OC stocks and potentially lead to wetland elevation loss and submergence, 2) in the absence of a change in saltwater intrusion, mangrove expansion can enhance OC storage 3) mangrove expansion can mitigate OC loss during saltwater intrusion, but this pattern depends on mangrove recruitment and ecosystem productivity.