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This study quantifies contributions of different food sources in the winter diet of the Velvet Scoter (Melanitta fusca) in coastal waters of the Lithuanian Baltic Sea using non-lethal avian sampling. We highlight the application of stable sulphur isotope ratios as complementary to stable carbon and nitrogen isotope analysis in order to discriminate sandy bottom macrozoobenthos organisms as potential food sources for the Velvet Scoter. Selection of the most relevant trophic enrichment factors and Monte Carlo simulations in order to choose the best fitted model were undertaken. The stable isotope mixing model revealed the main contributions of a group of bivalves, Mya arenaria and Cerastoderma glaucum, to be 46–54%, and while the crustacean, Saduria entomon, comprised 26–35% of the diet.