In this paper we present the results of analyses of stable carbon and nitrogen ratios in the bone collagen of prehistoric pinniped and sea otters from archaeological deposits in the Gulf of Alaska region. These data are useful as proxies of past changes in primary productivity and food web length, especially when considered in light of known paleoclimate episodes. We also present data on total mercury (tHg) values in these same samples demonstrating a relationship between isotopic signature, tHg, and paleoenvironmental change across the region. We discuss the need for long-term (paleo) observations of upper trophic levels, and the implications of these data for projecting ecosystem change under future climate scenarios.