Studies of current interactions among species, their prey, and environmental factors are essential for mitigating immediate threats to population viability, but the true range of behavioral and ecological flexibility can be determined only through research on deeper timescales. Ecological data spanning centuries to millennia provide important contextual information for long-term management strategies, especially for species that now are living in relict populations. Here we use a variety of methods to reconstruct bald eagle diets and local abundance of their potential prey on the Channel Islands from the late Pleistocene to the time when the last breeding pairs disappeared from the islands in the mid-20th century. Faunal and isotopic analysis of bald eagles shows that seabirds were important prey for immature/adult eagles for millennia before the eagles' local extirpation. In historic times (A.D. 1850-1950), however, isotopic and faunal data show that breeding bald eagles provisioned their chicks with introduced ungulates (e.g., sheep), which were locally present in high densities. Today, bald eagles are the focus of an extensive conservation program designed to restore a stable breeding population to the Channel Islands, but native and nonnative prey sources that were important for bald eagles in the past are either diminished (e.g., seabirds) or have been eradicated (e.g., introduced ungulates). In the absence of sufficient resources, a growing bald eagle population on the Channel Islands could expand its prey base to include carrion from local pinniped colonies, exert predation pressure on a recovering seabird population, and possibly prey on endangered island foxes.