Arctic organisms are exposed to various levels of pollutants, among which mercury (Hg) has raised important environmental concerns. Previous studies examining Hg levels, trends and effects on Arctic marine top-predators have focused on the Arctic region. However, many of these top-predators, such as seabirds, migrate to spend a large part of their life-cycle far from the Arctic in areas where their exposure to contaminants is largely unknown. By combining biotelemetry, Hg and stable isotope analyses, we studied the seasonal Hg contamination of little auks (Alle alle; the most abundant Arctic seabird) in relation to their distribution and marine foraging habitat, as well as its potential impacts on bird reproduction. We show that little auks were about 3.5 times more contaminated when outside the breeding season, and that Hg accumulated during this non-breeding non-Arctic period was related to egg size the following season with females having more Hg laying smaller eggs. Our results highlight that ecotoxicological studies should be expanded to yield a comprehensive understanding of contamination risks and associated threats to top-predators over their entire annual cycle. Furthermore, we show that an important non-breeding area located in the northwest Atlantic was associated with higher Hg contamination and demonstrate the utility of bird-borne miniaturized technology to evaluate the contamination of marine systems at large spatial scales.