This paper reports the occurrence of three new fish species, extremely rare in the Baltic Sea, and provides new data on their parasite fauna. The fish collected were Barbus barbus (Linnaeus, 1758), Salvelinus fontinalis (Mitchill, 1814), and Scophthalmus rhombus (Linnaeus, 1758). Their taxonomic identity was confirmed through genetic analyses using DNA extracted from fin clips. The stomach contents were examined, and age was determined by otolith or scale readings. Parasitological examinations focused on the skin, vitreous humour, eye lenses, mouth and nasal cavities, gills, gonads, viscera, and muscles. Furthermore, the changes of fish species composition over 20 years in Pomeranian Bay were analysed. The sequence comparisons against GenBank records revealed that sequences obtained for B. barbus and S. rhombus from Pomeranian Bay represent new rhodopsin barcodes. Record of the juvenile B. barbus in this study is the first in the Baltic Sea. Scophthalmus rhombus is a new host for the ciliate Trichodina jadranica, while Neogobius melanostomus (Pallas, 1814) is a new food item in the diet of S. rhombus in the Baltic Sea. Acanthocephalan Pomphorhynchus laevis found in the adult specimen of B. barbus and myxozoan Myxobolus musculi, noted in the juvenile specimen, have not been recorded previously in this fish species in Polish waters. Species collected as bycatch can potentially be used for monitoring potential changes in the overall fish community structure and biodiversity.