AbstractWe provide a 1‐year dataset of atmospheric surface CO2, CH4 and H2O concentrations and δ13C‐CO2 values from an Australian savanna site. These semi‐arid ecosystems act as carbon sinks in wet years but the persistence of the sink in dry years is uncertain. The dataset can be used to constrain uncertainties in modelling of greenhouse gas budgets, improve algorithms for satellite measurements and characterize the role of vegetation and soil in modulating atmospheric CO2 concentrations. We found pronounced seasonal variations in daily mean CO2 concentrations with an increase (by 5–7 ppmv) after the first rainfall of the wet season in early December with peak concentrations maintained until late January. The CO2 increase reflected the initiation of rapid microbial respiration from soil and vegetation sources upon initial wetting. As the wet season progressed, daily CO2 concentrations were variable, but generally decreased back to dry season levels as CO2 assimilation by photosynthesis increased. Mean daily concentrations of CH4 increased in the wet season by up to 0.2 ppmv relative to dry season levels as the soil profile became waterlogged after heavy rainfall events. During the dry season there was regular cycling between maximum CO2/minimum δ13C‐CO2 at night and minimum CO2/maximum δ13C‐CO2 during the day. In the wet season diel patterns were less regular in response to variable cloud cover and rainfall. CO2 isotope data showed that in the wet season, surface CO2 was predominantly a two‐component mixture influenced by C3 plant assimilation (day) and soil/plant respiration (night), while regional background air from higher altitudes represented an additional CO2 source in the dry season. Higher wind speeds during the dry season increased vertical mixing compared to the wet season. In addition, night‐time advection of high‐altitude air during low temperature conditions also promoted mixing in the dry season.