The carbon cycle in salt pans is complex and poorly understood. Field-based data are needed to improve regional estimates of C storage and land–atmosphere CO2 fluxes from dryland environments where pans are prevalent. This paper provides a first estimate of C stores and CO2 efflux within the salt pan, grassland and woodland of Ntwetwe Pan in the Makgadikgadi Basin, Botswana. C fluxes and stores associated with cyanobacteria-salt crusts are also determined. Total C stores are approximately an order of magnitude greater than on neighbouring Kalahari Sands at 675 ± 41, 760 ± 94 and 274 ± 15 tons ha− 1 to 1 m depth in the woodland, grassland and salt pan respectively. Most of the C is found as carbonate, with organic C comprising 4.6–10% of total C. CO2 efflux increased with temperature and also increased for a few hours after flooding of the pan surface. Crusts were a small net contributor to CO2 efflux in the dry season but could be a net CO2 sink in the wet season. The biogeochemistry of the sediment is likely to facilitate rapid conversion of organic C from aquatic organisms, biological crusts and algal mats into inorganic carbonates. Although further work is required to improve estimates of the spatial and temporal distribution of C, our data have demonstrated the substantial C store with the Makgadikgadi environment and the important role of biological crusts in the C cycle.