The Crozet Plateau is an area of interest as it is a region of the Southern Ocean where annual primary productivity is relatively high. We describe spatial and temporal variations in the biomarker distributions and carbon and nitrogen isotopic signatures of organic matter formed within surface waters around the plateau during an algal bloom. In the centre of the bloom, diatom-derived sterols dominate, whereas alkenones are relatively more abundant outside and at the edge of the bloom. Bulk organic δ13C and δ15N values are enriched inside the bloom area, ranging from −18.7‰ to −17.6‰ and +1.6‰ to +3.7‰, respectively, compared to −25.7‰ to −20.9‰ and −2.0‰ to +1.3‰, respectively, outside the bloom area. Variation in bulk δ15N values is attributed primarily to NH3 or dissolved organic N uptake, with only a minor contribution from Rayleigh fractionation of the pool. Compound specific δ13C values (cholest-5-en-3β-ol, cholesta-5,22-dien-3β-ol, 24-methylcholesta-5,22-dien-3β-ol, 24-methylcholesta-24(28)-dien-3β-ol and alkenones) are also enriched in the Fe fertilised region relative to other areas, presumably reflecting higher phytoplankton growth rate, consumption of dissolved inorganic carbon and perhaps more intense use of carbon concentrating mechanisms. The observations confirm previous interpretations that Fe fertilisation in the Crozet region has affected nutrient utilisation and the algal community structure; it also suggests that lipid biomarkers and their δ13C values record a specific bloom signature that may be recorded in underlying sediments.