Quantifying carbon storage in coastal wetland environments is important for identifying areas of high carbon sequestration value that could be targeted for conservation. This study combines remote sensing and sediment analysis to identify spatial variation in soil carbon storage for Currambene Creek, New South Wales, Australia to establish whether vegetation structure influences soil carbon storage in the upper 30 cm. Wetland vegetation was delineated to capture structural complexity within vegetation communities using Light detection and ranging (Lidar) point cloud data and aerial imagery with an object-based image analysis approach. Sediment cores were collected and analysed for soil carbon content to quantify below-ground carbon storage across the site. The total soil carbon storage in the upper 30 cm for the wetland (59.6 ha) was estimated to be 3933 ± 444 Mg C. Tall mangrove were found to have the highest total carbon storage (1420 ± 198 Mg C), however are particularly sensitive to changes in sea-level as they are positioned lowest in the intertidal frame. Conservation efforts targeted at protecting areas of high carbon sequestration, such as the tall mangrove, will lead to a greater contribution to carbon mitigation efforts.