The protection of carbon (C) stores in the form of remnant native vegetation and soils is crucial for minimising C emissions entering the atmosphere. This study estimated C storage in soils, woody vegetation, dead standing vegetation, coarse woody debris, herbaceous vegetation, litter and roots in plant communities commonly encountered on cotton farms. River red gum was the most valuable vegetation type for C storage, having up to 4.5% C content in the surface (0–5 cm) soil, a total-site C store of 216 ± 28 t ha^–1 (mean ± s.e.) and a maximum value of 396.4 t C ha^–1. Grasslands were the least C-dense, with 36.4 ± 3.72 t C ha^–1. The greatest proportion of C in river red gum sites was in standing woody biomass, but in all other vegetation types and especially grasslands, the top 0–30 cm of the soil was the most C-rich component. Aboveground woody vegetation determined total-site C sequestration, as it strongly influenced all other C-storing components, including soil C. This study illustrates the value of native vegetation and the soil beneath for storing large amounts of C. There is a case for rewarding farmers for maintaining and enhancing remnant vegetation to avoid vegetation degradation and loss of existing C stores.