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This study explores the changes in the surface water fugacity of carbon dioxide (fCO2) and biological carbon uptake in two Southern Ocean iron fertilisation experiments with different hydrographic regimes. The Southern Ocean Iron Release Experiment (SOIREE) experiment was carried out south of the Antarctic Polar Front (APF) at 61°S, 141°E in February 1999 in a stable hydrographic setting. The EisenEx experiment was conducted in a cyclonic eddy north of the APF at 48°S, 21°E in November 2000 and was characterised by a rapid succession of low to storm-force wind speeds and dynamic hydrographic conditions. The iron additions promoted algal blooms in both studies. They alleviated algal iron limitation during the 13-day SOIREE experiment and probably during the first 12 days of EisenEx. The fCO2 in surface water decreased at a constant rate of 3.8μatmday−1 from 4 to 5 days onwards in SOIREE. The fCO2 reduction was 35μatm after 13 days. The evolution of surface water fCO2 in the iron-enriched waters (or ‘patch’) displayed a saw tooth pattern in EisenEx, in response to algal carbon uptake in calm conditions and deep mixing and horizontal dispersion during storms. The maximum fCO2 reduction was 18–20μatm after 12 and 21 days with lower values in between. The iron-enriched waters in EisenEx absorbed four times more atmospheric CO2 than in SOIREE between 5 and 12 days, as a result of stronger winds. The total biological uptake of inorganic carbon across the patch was 1389ton C (±10%) in SOIREE and 1433ton C (±27%) in EisenEx after 12 days (1ton=106g). This similarity probably reflects the comparable size of the iron additions, as well as algal growth at a similar near-maximum growth rate in these regions. The findings imply that the different mixing regimes had less effect on the overall biological carbon uptake across the iron-enriched waters than suggested by the evolution of fCO2 in surface water.