Natural iron fertilisation from Southern Ocean islands results in high primary production and phytoplankton biomass accumulations readily visible in satellite ocean colour observations. These images reveal great spatial complexity with highly varying concentrations of chlorophyll, presumably reflecting both variations in iron supply and conditions favouring phytoplankton accumulation. To examine the second aspect, in particular the influences of variations in temperature and mixed layer depth, we deployed four autonomous profiling floats in the Antarctic Circumpolar Current near the Kerguelen Plateau in the Indian sector of the Southern Ocean. Each "bio-profiler" measured more than 250 profiles of temperature (T), salinity (S), dissolved oxygen, chlorophyll a (Chl a) fluorescence, and particulate backscattering (bbp) in the top 300 m of the water column, sampling up to 5 profiles per day along meandering trajectories extending up to 1000 km. Comparison of surface Chl a estimates (analogous to values from satellite images) with total water column inventories revealed largely linear relationships, suggesting that these images provide credible information on total and not just surface biomass spatial distributions. However, they also showed that physical mixed layer depths are often not a reliable guide to biomass distributions. Regions of very high Chl a accumulation (1.5–10 μg L−1) were associated predominantly with a narrow T–S class of surface waters. In contrast, waters with only moderate Chl a enrichments (0.5–1.5 μg L−1) displayed no clear correlation with specific water properties, including no dependence on mixed layer depth or the intensity of stratification. Geostrophic trajectory analysis suggests that both these observations can be explained if the main determinant of biomass in a given water parcel is the time since leaving the Kerguelen Plateau. One float became trapped in a cyclonic eddy, allowing temporal evaluation of the water column in early autumn. During this period, decreasing surface Chl a inventories corresponded with decreases in oxygen inventories on sub-mixed-layer density surfaces, consistent with significant export of organic matter (~35%) and its respiration and storage as dissolved inorganic carbon in the ocean interior. These results are encouraging for the expanded use of autonomous observing platforms to study biogeochemical, carbon cycle, and ecological problems, although the complex blend of Lagrangian and Eulerian sampling achieved by the floats suggests that arrays rather than single floats will often be required, and that frequent profiling offers important benefits in terms of resolving the role of mesoscale structures on biomass accumulation.