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Cormorants roosting in open sea move to inland freshwater bodies, their trophic niche overlapping that of individuals settled there. Similarly, individuals settled around transitional waters (coastal lagoon), seem to divide the predation pressure between different food sources along the marine-continental gradient. Recently in Spain, the Great Cormorant has been devoid of legal protection due to its supposed impact on fisheries. Our methods provide a useful and non-invasive tool that can be used as a first step for assessing such interaction. 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