The eastern Bering is a productive high-latitude ecosystem characterized by high interannual variability in physical environmental conditions that impact biological communities. We investigated how the diet composition of northern fur seals (Callorhinus ursinus) breeding on the Pribilof Islands was influenced by this variation, focusing on water temperatures (surface and bottom) and an index of walleye pollock abundance within foraging areas. We also explored whether interannual variation in diet composition influenced fur seal pup mortality rates or weights. The frequency of occurrence (FO) of seven (of eight) fur seal prey groups detected from hard parts analysis of samples collected from 1987 to 2012 was affected by interannual variation in at least one of the three environmental variables. Of particular note was the decrease in pollock FO as pollock abundance within foraging areas decreased, as pollock is one of the most important fur seal prey species in this region and projected to decline considerably in the coming decades. A considerable amount of variation in FO of almost all prey groups was explained by year effects, suggesting that water temperatures alone were not sufficiently capturing the influences of regional and local physical environmental conditions on prey availability for fur seals. The summed FO of non-pollock prey groups had a small but detectable effect on pup mortality rates, indicating that availability of prey groups beyond just pollock are somewhat beneficial for female northern fur seals early in lactation. Our results suggest that projected environmental changes in the eastern Bering Sea are likely to influence fur seal diets, but predicting the magnitude and direction of such changes is hampered until the underlying drivers of the observed temporal trends are better resolved.