Prey choice of opportunistic piscivorous birds, such as Phalacrocoracidae, may primarily depend on prey abundance in rivers. Estuaries, the most downstream river stretches, often represent important feeding sites for piscivorous birds, but are usually characterised by highly dynamic fish assemblages. Thus, studies of the composition of diets of estuarine birds also require up-to-date information on prey abundances. In this study, interactions between diet composition and prey abundance by species and size were investigated for the great cormorant Phalacrocorax carbo in the natural setting of a typical European estuary. Moderate to high overlap between diet composition and estuarine prey abundances indicated that prey abundance represented the major factor driving prey choice of cormorants. However, differences in length distributions between cormorant diet and estuarine fish fauna suggested that prey size in particular species was another factor influencing prey choice of cormorants. While small-sized individuals of main prey species, especially European smelt Osmerus eperlanus, were underrepresented, large-sized individuals of twaite shad Alosa fallax were overrepresented in the cormorant diet. Flexible selection of prey in relation to particular species and size classes may be the result of the superabundance of potential prey in a highly productive environment such as an estuary.