Molecular scatology and next-generation sequencing identified previously unknown linkages among ecosystems in the diet of Semipalmated Sandpipers (Calidris pusilla) in the Bay of Fundy, Canada. During their annual migratory stopover, the birds consumed a wider range of prey items than previously reported, which suggests that they are not selecting for the amphipod Corophium volutator and are acting as generalist foragers. Our analysis identified several novel prey items—arachnids, crabs, bivalves, several terrestrial and freshwater insect species, ctenophores, cnidarians, and fish (likely eggs or juveniles)—indicating that Semipalmated Sandpipers consume prey from marine, freshwater, and terrestrial ecosystems. Connections between Semipalmated Sandpipers and freshwater and terrestrial ecosystems were previously unknown in the Bay of Fundy. Current conservation efforts for this species are focused on beach and intertidal habitats; however, we may also need to consider the surrounding freshwater and terrestrial habitat.