The soil in terrestrial and blue carbon ecosystems (BCE; mangroves, tidal marshes, seagrasses) is a significant carbon (C) sink. National assessments of C inventories are needed to protect them and aid nature-based strategies to sequester atmospheric carbon dioxide. We harmonised measurements from Australia's terrestrial and BCE and, using consistent multi-scale spatial machine learning, unravelled the drivers of soil organic carbon (SOC) variation and digitally mapped their stocks. The modelling shows that climate and vegetation are continentally the primary drivers of SOC variation. But the underlying regional drivers are ecosystem type, terrain, clay content, mineralogy, and nutrients. The digital soil maps indicate that in the 0-30 cm soil layer, terrestrial ecosystems hold 27.6 Gt (19.6-39.0 Gt), and BCE 0.35 Gt (0.20-0.62 Gt). Tall open eucalypt and mangrove forests have the largest mean SOC per unit area. Eucalypt woodlands and hummock grassland, which occupy vast areas, store the largest total SOC stock. These ecosystems constitute important regions for conservation, emissions avoidance, and preservation because they also provide additional co-benefits.

Soil collection and analysis of chemical and physical attributes was carried out at the Great Western Woodlands site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project.

Soil collection and analysis of chemical and physical attributes was carried out at the Calperum Mallee site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project.

Soil collection and analysis of chemical and physical attributes was carried out at the Litchfield Savanna site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project.

Soil collection and analysis of chemical and physical attributes was carried out at the Whroo Dry Eucalypt site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project.

Soil collection and analysis of chemical and physical attributes was carried out at the Samford Peri-Urban site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project.

Soil collection and analysis of chemical and physical attributes was carried out at the Alice Mulga site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project.

Soil collection and analysis of chemical and physical attributes was carried out at the Robson Creek Rainforest site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project.

Soil collection and analysis of chemical and physical attributes was carried out at the Warra Tall Eucalypt site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project.

Soil collection and analysis of chemical and physical attributes was carried out at the Karawatha Peri-Urban site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project.