The interannual variability of net community production (NCP) and air-sea CO2 flux in a naturally iron fertilized and productive area of the Southern Ocean (Kerguelen plateau) was investigated using a 1D biogeochemical model driven by satellite chlorophyll, sea surface temperature and wind speed data for the 1997–2007 period. The model simulates the low fCO2 and dissolved inorganic carbon (DIC) measured during summers 2004–05, 2005–06, 2006–07 and the high NCP derived from a seasonal carbon budget in the surface waters of these blooms. Although satellite data show high interannual variability in the dynamics and magnitude of the bloom during the 1997–2007 decade, the simulated interannual variability of the NCP was only ± 14%. This unexpected result could be due to the combined effect of both the duration and the start date of the bloom, the latter determining the depth of the mixed layer used to compute the NCP. In the productive area, the interannual variability of air-sea CO2 flux (± 13%) was not only driven by the biological effect but also by the solubility effect. Our results contrast with previous studies in the high nutrient, low chlorophyll regions of the Southern Ocean.