This paper presents information on the levels of trace elements in sediments collected at Deception and Penguin Islands and tracks the sources of natural and anthropogenic inputs of metals into this sub-Antarctic region. The results suggest that natural processes, such as volcanic activity, hydrothermal processes and sediment transport, are more important than anthropogenic inputs in accounting for the metal concentrations measured in sediments at Deception Island. The higher levels of trace metals recorded in sediments at Penguin Island seem to reflect the composition of the source rocks of the island, which are dominated by the olivine-basalt group. Our findings show that human activities in the study areas may contribute to negligible levels of trace metals associated with anthropogenic inputs (e.g., Cr and Zn) in sediments, and these results can be used in the future as background levels related to low anthropogenic impacts.