Contamination in marine foodwebs is nowadays of great environmental concern owing to the increasing levels of pollution in marine ecosystems from different anthropogenic sources. Seabirds can be used as indicators of regional contaminant patterns across large temporal and spatial scales. We analysed Hg, Se and Pb levels as well as stable isotope ratios of C (13C/12C, δ13C) and N (15N/14N, δ15N) in breeding- and winter-season feathers on males and females of two related shearwater species, providing information on spatiotemporal patterns of contaminants as well as the influence of the trophic ecology of these seabirds on contaminant levels. During the breeding season, Se and Pb concentrations were highest at the Cape Verde archipelago, showing no differences among the other colonies or between the sexes. However, Hg levels varied among colonies, being highest in the Mediterranean, probably resulting from the larger emissions and fallout of this pollutant in Europe. Feathers grown during breeding also showed sexual differences in Hg concentrations and δ13C. Differences in Hg concentration between sexes are mainly due to egg-laying decontamination in females. In contrast, differences in Hg among colonies are probably related to differences in trophic ecology, as indicated by δ13C and δ15N measurements. Contaminant concentrations in winter-grown feathers did not show any relationship with stable isotope values but were affected by contaminant loads associated with the breeding season. These findings suggest that the interpretation of contaminant levels of migratory species from feathers moulted out of the breeding season should be made with caution because those values could reflect exposures to contaminants acquired during the breeding season. We conclude that factors other than feeding ecology may play an important role in the interpretation of contaminant levels and their annual dynamics at several spatial scales. Consideration of the relevant temporal context provided by isotopic signatures and contaminant concentrations is important in deciphering contaminant information based on various tissues.