A total of 72 specimens of Babka gymnotrachelus (Kessler, 1857), Neogobius fluviatilis (Pallas, 1814), and Neogobius melanostomus (Pallas, 1814) from four sampling sites along the Bulgarian section of the Danube River (Kudelin, Novo selo, Koshava, and Kutovo), Northwestern Bulgaria were submitted to ecologohelminthological investigation. During the examination 6 species of helminths have been identified from 3 classes: Trematoda (Nicolla skrjabini (Iwanitzky, 1928) Dollfus, 1960), Acanthocephala (Acanthocephalus anguillae (Müller, 1780) Lühe, 1911; Acanthocephalus lucii (Müller, 1776) Lühe, 1911; Pomphorhynchus laevis (Zoega in Müller, 1776) Porta, 1908) and Nematoda (Contracaecum sp., Eustrongylides excisus Jägerskiöld, 1909). Ecological indices of the established endohelminth species were tracked. The four sampling sites from the Danube River are new habitats for the discovered endohelminth species of racer goby, monkey goby, and round goby. The three goby species are new host records: B. gymnotrachelus and N. fluviatilis for Ac. lucii; N. melanostomus for Ac. lucii, Ac. anguillae and Contracaecum sp. New species of helminths are found in the helminth fauna of the three studied species of gobies from the Danube River and the river basin (Ac. lucii of N. fluviatilis) and in Bulgaria (Ac. lucii of B. gymnotrachelus; Ac. lucii, Ac. anguillae and Contracaecum sp. of N. melanostomus). The pathogenic species helminths for the fish and humans are found.