Saltmarsh and mangrove ecosystems play an important role in climate change mitigation as a nature-based solution, while providing additional ecosystem services. Commonly referred to as ‘blue carbon’ (BC) ecosystems, they sequester and store larger volumes of carbon per unit area than other vegetated environments, the most significant storage pool being in the soil. Understanding the drivers of variability in BC soil stocks is crucial to providing accurate carbon accounting and effective management of saltmarsh and mangrove habitats for carbon abatement. We aimed to determine the primary factors influencing soil carbon stocks to assist in calculating accurate baseline estimates and inform management and restoration activities. We sampled soil carbon stocks from sites with long-term vegetation survey data and high-resolution elevation data. In total 72 soil cores were taken across South Australia within three vegetation communities (mangrove, intertidal saltmarsh and supratidal saltmarsh). We found soil type and elevation to be strong predictors of soil carbon, with some sites having a more complex dynamic with geomorphology and vegetation type contributing to variability in stocks. Using this information to inform management decisions around tidal reconnection and coastal wetland habitat restoration and protection will allow the greatest benefits to be achieved for climate change mitigation.