Biogenic silica stocks and fluxes were investigated in austral summer over the naturally iron-fertilized Kerguelen Plateau and in nearby high-nutrient, low-chlorophyll (HNLC) off-plateau surface waters. The Kerguelen Plateau hosted a large-diatom bloom, with high levels of biogenic silica (BSi) but relatively low silicic acid (Si(OH)4) uptake rates (1100±600 mmol m−2 and 8±4 mmol m−2 d−1, respectively). Diatoms of the naturally iron-enriched area presented high affinities for silicic acid, allowing them in combination with a beneficial nutrient vertical supply to grow in low silicic acid waters (<2 μM). Si(OH)4 acid uptake rates were also compared with carbon and nitrogen uptake rates. As expected for diatoms growing in favourable nutrient conditions, and from previous artificial iron-enrichment experiments, Si:C and Si:NO3 elemental uptake ratios of the natural diatom community of the plateau were close to 0.13 and 1, respectively. In contrast, diatom communities in the HNLC waters were composed of strongly silicified (high Si:C, Si:NO3 uptake ratios) diatoms with low affinities for Si(OH)4. Although the Si:NO3 uptake ratio in the surface waters of the plateau was close to 1, the apparent consumption of nitrate on a seasonal basis was much lower (∼5 μM) than the apparent consumption of silicic acid (∼15 μM). This was mainly due to diatoms growing actively on ammonium (i.e. 39–77% of the total nitrogen uptake) produced by an intense heterotrophic activity. Thus we find that while Fe fertilization does increase N uptake with respect to Si uptake, rapid recycling of N decouples nitrogen and carbon export from silica export so that the “silicate pump” remains more efficient than that of N (or P). For this reason an iron-fertilized Southern Ocean is unlikely to experience nitrate exhaustion or export silicic acid to the global ocean.