This dataset includes all the Fe(II) measurements carried out during the LOHAFEX ocean iron fertilization (January- March 2009) in waters of a stable eddy located in the Atlantic sector of the Southern Ocean. Data serve the purpose to compare the effect of physicochemical and biological variables in changes in the proportion of Fe(II)/Fe(III) concentrations during the development of a flagellate/copepod bloom. Measurements were performed with a flow injection system where seawater is mixed with an alkaline luminol solution that emits lights proportionally to the concentration of reduced iron (Fe(II)). Data are split in one file showing Fe(II) concentrations before and after filtration through 0.2 mm in the upper 200 m of the water column and several files showing Fe(II) concentrations in unfiltered seawater collected with the underway sampling (11 m deep) while sailing across the fertilized patch. This is the first data sets that address the contribution of particles to Fe(II) concentrations in seawater. Transect Fe(II) data are accompanied by photosynthetic quantum efficiency (FV/FM) and chlorophyll-a data that allow the precise location of the fertilized patch edge.