Iron is the limiting micronutrient in the Southern Ocean and experiments have demonstrated that addition of soluble iron to surface waters results in phytoplankton blooms, particularly by large diatoms. Antarctic krill (Euphausia superba) eat diatoms and recycle iron in surface waters when feeding. Baleen whales eat krill, and, historically, defecation by baleen whales could have been a major mechanism for recycling iron, if whale faeces contain significant quantities of iron. We analysed the iron content in 27 samples of faeces from four species of baleen whale. Faecal iron content (145.9 ± 133.7 mg kg−1) is approximately ten million times that of Antarctic seawater, suggesting that it could act as a fertilizer. Furthermore, we analysed the iron content of seven krill species and of muscle tissue of two species of baleen whales; all samples had high iron levels. Using these figures, together with recent estimates of the range and biomass of krill, we calculate that the Antarctic krill population contains ∼24% of the total iron in the surface waters in its range. Thus, krill can act as a long-term reservoir of iron in Antarctic surface waters, by storing the iron in their body tissue. Pre-exploitation populations of whales and krill must have stored larger quantities of iron and would have also recycled more iron in surface waters, enhancing overall ocean productivity through a positive feedback loop. Thus, allowing the great whales to recover might actually increase Southern Ocean productivity through enhancing iron levels in the surface layer.