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Mercury (Hg) can be neurotoxic to mammals and impact reproduction, whereas selenium (Se) is an important antioxidant known to ameliorate some adverse effects of Hg. Total Hg concentrations ([THg]) were measured in lanugo (pelage grown in utero) of 812 Steller sea lion (Eumetopias jubatus) pups across Alaska and Russia to assess fetal exposure during late gestation. The molar ratio of total Se to THg (TSe:THg) was determined in whole blood collected from 291 pups. Stable isotope ratios of carbon and nitrogen were measured in sections of vibrissae (whiskers, n = 498) and in lanugo (n = 480) of pups grown during late gestation to track diet variations among adult females that can drive Hg and Se exposure during this critical fetal development period. Lanugo [THg] ranged from 1.4 to 73.7 μg/g dry weight with the lowest median [THg] in Southeast Alaska. Pups from the Western Aleutian Islands had higher median lanugo [THg] than pups from other metapopulations in Alaska. Over 25% of pups in the Western Aleutian Islands had [THg] above published risk thresholds (20 μg/g) for other mammals. Whole blood molar TSe:THg was significantly lower in the Western Aleutian Islands and in some parts of the Central Aleutian Islands with higher molar ratios found in the Eastern Aleutian Islands and Central Gulf of Alaska. This suggests a limitation on potential protective functions of Se in the western regions with the highest relative [THg]. The Central Aleutian Island pups with [THg] over 20 μg/g had higher δ15N ratios than pups with lower [THg] suggesting dams consuming higher trophic level prey is a key driver for Hg exposure. However, regional differences likely reflect variability in diet of the dam during gestation and in Hg food web dynamics between oceanic regimes east and west of key passes in the Aleutian Islands. Unlabelled Image • Steller sea lions were studied from Alaska across the Aleutian Islands to Russia. • δ15N and δ13C were used to understand feeding ecology drivers of Hg and Se concentrations. • >25% of Western Aleutian Island pups had [THg] above adverse risk thresholds. • Pups with highest [THg] showed increased risk of Hg-dependent Se deficiency. • Pregnant dam diet and food web dynamics are regionally dependent. [ABSTRACT FROM AUTHOR]