Although climate change occurs alongside other anthropogenic ecosystem impacts, little is known about how sea-surface temperature variability influences the ecotoxicology of persistent organic pollutants (POPs). We analyzed POP contaminant levels, and stable isotopes δ15N and δ13C as measures of trophic position, in eggs collected from the Gulf of Alaska and Bering Sea between 1999 and 2010 from two similar avian species with different trophic positions: common murres (Uria aalge) and thick-billed murres (Uria lomvia). The ebb and flow of the Pacific Decadal Oscillation (PDO), a long-lived El Niño-like pattern of climate variability in the Pacific Ocean, predicted both trophic position and polychlorinated biphenyl (PCB) levels in thick-billed murres, but not in common murres. There was a similar pattern of association of the PDO with organochlorine pesticide levels in thick-billed murres, but not in common murres. The magnitude of association in thick-billed murres of PDO with the level of a specific PCB congener was a function of the number of chlorine groups on the PCB congener. Although this statistical analysis does not account for all factors contributing to climate variation, this contrast between the species suggests that facultative changes in foraging behavior, reflected in trophic position, can determine how POPs flow through and thereby alter ecosystems under climate change.