Marine food webs in coastal southern South America are thought to have been impacted over time in response to humans in the late Holocene to the Anthropocene. Archaeological sites on the coast of Tierra del Fuego, Argentina, provide a biogeochemical record that can potentially inform us about ecological dynamics over this time period. This record appears as bone collagen from Otariids, southern fur seals (Arctocephalus australis) and sea lions (Otaria flavescens), high trophic level predators. To quantify ecological relationships, we measured bulk and compound specific stable isotope ratios from organic tissues in Otariids and several other associated animals, several of which were potential otariid prey and basal food web resources. Variations in bulk stable isotope ratios of carbon and nitrogen are linked to potential dietary differences and habitat specialization (coastal areas or open ocean) in populations ranging in age from 7000 cal. years BP to the modern day. We observed increases in the variability of these isotopic compositions over time, which suggests a diversity in the diets and habitats of Otariids. Shifts in marine food webs occurred during the transition from subsistence hunting of Otariids to industrial hunting and expanded human influence. δ13C ratios of amino acids suggest shifts from coastal to offshore foraging in otariids from past to present, while δ15N in amino acids showed little change in overall ecological baseline shifts but large variation in trophic level and foraging location in individual otariids. δ2H dynamics in amino acids largely corroborated results found in δ13C and δ15N amino acids. We conclude that direct human influences, such as hunting and habitat alteration, were the major drivers of ecological change in southern South American marine ecosystems rather than climate change.