To date the studies that link community structure of benthic invertebrates with fish feeding are rare as well as factors that are behind this feeding selectivity are poorly known. In this study, we related invertebrate species composition, their dominance structure and fish biological characteristics to the feeding selectivity and overlap of the native flounder, perch and the invasive round goby in Muuga Bay, the Baltic Sea. Species composition and proportion of benthic invertebrates in the diet of fishes differed from what was available in the field. Except for the round goby, the studied fishes preferred small and mobile invertebrates over large bivalves. However, diet of the studied species, namely the round goby and flounder overlapped. Besides, perch preyed on young stages of the round goby indicating that the introduction of round goby may negatively affect flounder but positively perch.