Seabirds from remote regions are mainly exposed to environmental contaminants from non-point contamination of their food webs. Pre-fledging seabird chicks are fed by their parents with marine prey captured in the vicinity of breeding colonies. Contaminant concentrations in tissues of pre-fledging chicks can thus be mostly related to local dietary sources, and have the potential to unravel spatial patterns of environmental contamination in marine ecosystems. Here, mercury (Hg), 13 other trace elements, and 18 persistent organic pollutants (POPs) were quantified in blood of chicks across four breeding locations that encompass a large latitudinal range in the southern Indian Ocean (from Antarctica, through subantarctic areas, to the subtropics), over a single breeding season. Thirteen species of penguins, albatrosses and petrels were studied, including endangered and near-threatened species, such as Amsterdam albatrosses and emperor penguins. Blood Hg burdens varied widely between species, with a factor of ~50 between the lowest and highest concentrations (mean ± SD, 0.05 ± 0.01 and 2.66 ± 0.81 µg g−1 dry weight, in thin-billed prions and Amsterdam albatrosses, respectively). Species relying on Antarctic waters for feeding had low Hg exposure. Concentrations of POPs were low in chicks, with the exception of hexachlorobenzene. Contaminant concentrations were mainly explained by species differences, but feeding habitat (inferred from δ13C values) and chicks’ body mass also contributed to explain variation. Collectively, our findings call for further toxicological investigations in Amsterdam albatrosses and small petrel species, because they were exposed to high and diverse sources of contaminants, and in macaroni penguins, which specifically showed very high selenium concentrations. Capsule: Seabird chicks from four distant sites in the southern Indian Ocean had contrasted blood metallic and organic contaminant patterns depending on species, feeding habitat and body mass.