Submerged aquatic vegetation (SAV) thrives across the estuarine salinity gradient providing valuable ecosystem services. Within the saline portion of estuaries, seagrass areas are frequently cited as hotspots for their role in capturing and retaining organic carbon (C_org). Non-seagrass SAV, located in the fresh to brackish estuarine areas, may also retain significant soil C_org, yet their role remains unquantified. Given rapidly occurring landscape and salinity changes due to human and natural disturbances, landscape level carbon pool estimates from estuarine SAV habitat blue carbon estimates are needed. We assessed C_org stocks in SAV habitat soils from estuarine freshwater to saline habitats (interior deltaic) to saline barrier islands (Chandeleur Island) within the Mississippi River Delta Plain (MRDP), Louisiana, USA. SAV habitats contain C_org stocks equivalent to those reported for other estuarine vegetation types (seagrass, salt marsh, mangrove). Interior deltaic SAV C_org stocks (231.6 ± 19.5 Mg C_org ha⁻¹) were similar across the salinity gradient, and significantly higher than at barrier island sites (56.6 ± 10.4 Mg C_org ha⁻¹). Within the MRDP, shallow water SAV habitat covers up to an estimated 28,000 ha, indicating that soil C_org storage is potentially 6.4 ± 0.1 Tg representing an unaccounted C_org pool. Extrapolated across Louisiana, and the Gulf of Mexico, this represents a major unaccounted pool of soil C_org. As marshes continue to erode, the ability of coastal SAV habitat to offset some of the lost carbon sequestration may be valuable. Our estimates of C_org sequestration rates indicated that conversion of eroding marsh to potential SAV habitat may help to offset the reduction of C_org sequestration rates. Across Louisiana, we estimated SAV to offset this loss by as much as 79,000 Mg C yr⁻¹ between the 1960s and 2000s.