This is the first comprehensive study covering the parasite fauna of smelt, Osmerus eperlanus, from five estuary sites of the southern Baltic Sea in a stretch of almost 500 km. We examined 432 smelt from: the Neman River mouth, the Vistula River mouth, Pomeranian Bay, the Oder River, and Lake Dąbie and recovered 13 species/higher-rank taxa of parasites: Diplostomum spp., Posthodiplostomum cuticola, Eubothrium crassum, Proteocephalus longicolis, Cystidicola farionis, Hysterothylacium aduncum, Corynosoma semerme, Pomphorhynchus laevis, Unionidae gen sp., Ergasilus sieboldi, Argulus foliaceus, Piscicola geometra, and Saprolegniaceae gen sp. Basic infection parameters such as prevalence, intensity of infection, mean intensity of infection, and the dominance index were determined. The findings of the presently reported study constitute a number of new faunistic records. There were two new host records (Posthodiplostomum cuticola and Saprolegniaceae gen sp.), five new host records for Poland (Diplostomum spp., Pomphorhynchus laevis, Piscicola geometra, Argulus foliaceus, and Unionidae gen sp.), and two new host records for Lithuania (Argulus foliaceus and Unionidae gen sp.). We carefully analyzed the relevant information from more than 100 publications on smelt parasites to compare the data with our own findings.