Anthropogenic interference is a major driver of ecological change in freshwater ecosystems. Pollution and the introduction of new species not only alter macrozoobenthic community structures, but can also affect their respective parasite communities. The ecology of the Weser river system experienced a drastic decline in biodiversity over the past century due to salinization caused by the local potash industry. As a response, the amphipod Gammarus tigrinus was released into the Werra in 1957. A few decades after the introduction and subsequent spread of this North American species, its natural acanthocephalan Paratenuisentis ambiguus was recorded in the Weser in 1988, where it had captured the European eel Anguilla anguilla as a novel host. To assess the recent ecological changes in the acanthocephalan parasite community, we investigated gammarids and eel in the Weser river system. In addition to P. ambiguus, 3 Pomphorhynchus species and Polymorphus cf. minutus were discovered. The introduced G. tigrinus serves as a novel intermediate host for the acanthocephalans Pomphorhynchus tereticollis and P. cf. minutus in the tributary Werra. Pomphorhynchus laevis is persistent in the tributary Fulda in its indigenous host Gammarus pulex. Pomphorhynchus bosniacus colonized the Weser with its Ponto-Caspian intermediate host Dikerogammarus villosus. This study highlights the anthropogenically driven changes in ecology and evolution in the Weser river system. Based on morphological and phylogenetic identification, the shifts in distribution and host usage described here for the first time contribute to the puzzling taxonomy of the genus Pomphorhynchus in times of ecological globalization.