Soils in terrestrial and coastal blue carbon ecosystems are an important carbon sink. National carbon inventories require accurate assessments of soil carbon in these ecosystems to aid conservation and nature-based climate change mitigation strategies. Here we harmonise measurements from Australia’s terrestrial and blue carbon ecosystems and apply a multiscale spatial machine learning model to estimate soil carbon stocks and drivers of variation. We find that climate and vegetation are the primary drivers of variation at the continental scale, with ecosystem type, terrain, clay content, mineralogy and nutrients drive subregional variations. We estimate that in the top 0–30cm soil layer, terrestrial ecosystems hold 27.6 Gt C (19.6–39.0 Gt C), and blue carbon ecosystems hold 0.35 GtC (0.20–0.62 GtC). Tall open eucalypt and mangrove forests have the largest soil carbon content by area, while eucalypt woodlands and hummock grasslands have the largest total carbon stock due to their large area. Our findings suggest these are important ecosystems for conservation and nature-based mitigation climate change strategies.