Estuaries are ‘hot spots’ in the global carbon cycle, yet data on carbon dynamics, in particular air‐sea CO2 fluxes, from autotrophic systems are rare. Estuarine carbon budgets were constructed for three geomorphically distinct warm temperate Australian estuaries over an annual cycle. All three estuaries were net autotrophic, with annual net ecosystem metabolism (NEM) ranging from 8 ± 13.4 molC m−2 yr−1 to 10 ± 14 molC m−2 yr−1. There was a net flux of CO2 from the atmosphere to the estuaries of between 0.4 ± 0.6 molC m−2 yr−1 and 2 ± 0.9 molC m−2 yr−1. Loading of dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) to the estuaries varied markedly within and between the estuaries, and was directly related to freshwater inflow. While NEM was similar in all three estuaries, the ratio of benthic versus pelagic contributions to NEM differed, with NEM dominated by pelagic production in the river dominated system, benthic production dominating in the intermediate estuary, and equal contributions of benthic and pelagic production in the marine dominated lagoon. All three estuaries exported more organic carbon than was imported, fueled by additional organic carbon supplied by NEM. The estuaries essentially acted as bioreactors, transforming DIC to organic carbon. Burial of organic carbon ranged from 1.2 ± 0.3 molC m−2 yr−1 to 4.4 ± 1.2 molC m−2 yr−1 and represented up to half of NEM. The annual net uptake of atmospheric CO2 in these systems, along with previous estimates of the global estuarine CO2flux being based predominantly on heterotrophic, large river dominated estuarine systems, indicates that the global estimate of the estuarine air‐water CO2flux may be over‐estimated due to the lack of studies from autotrophic marine dominated estuaries.