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The aim of the present study was to determine the concentrations of nonylphenols (NPs) and 4-t-octylphenol (4tOP) in the muscles, liver, and kidneys of selected waterbird species. Three species with different feeding habits were selected, i.e., greater scaup (Aythya marila), great crested grebe (Podiceps cristatus), and great cormorant (Phalacrocorax carbo) to investigate the potential effects of diet on the level of contaminants tested. The determination and quantification of analytes were performed using gas chromatography with mass spectrometric detection (GC-MS). The highest NP concentrations were noted in the kidneys of greater scaups and great crested grebes (208.3 and 160.8 μg kg−1 ww, resp.), which were six to fourteen-fold higher than those in the muscles (15.0 and 25.6 μg kg−1 ww, resp.) and livers (22.9 and 13.8 μg kg−1 ww, resp.) of these species. In greater scaups, the mean concentration of NPs in the livers was lower than in the muscles, while in great crested grebes, it was the opposite and higher concentrations were noted in the muscles. The mean concentrations of NPs in the muscles and livers of great cormorants were at similarly low levels (12.5 and 9.7 μg kg−1 ww, resp.). The concentrations of 4tOP in all samples were low, ranging from