Data from a long-term study of the intestinal helminth parasite community of eels, Anguilla anguilla, stocked into the shallow eutrophic Neusiedler See, Austria, were collected over an 8 year period (1994–2001). In total, 720 eels from 2 sampling sites were examined. The parasite community showed characteristics similar to those in the natural eel populations in rivers of the UK and mainland Europe: it was species poor, with only 5 species (Acanthocephalus lucii, Acanthocephalus anguillae, Raphidascaris acus, Proteocephalus macrocephalus, Bothriocephalus claviceps) comprising the component community and a maximum infracommunity richness of 4 species. Over the period, the intestinal parasite community of the sampling site in Illmitz, which was originally dominated by A. lucii, changed. As levels of A. anguillae increased to a point at which it dominated the community, diversity increased whilst dominance of a single species decreased. By contrast the community in the southern sampling site remained rather constant with a continuous high infection level of A. anguillae and low abundance of A. lucii. Both acanthocephalan species exhibited higher infection levels in larger eels and in different seasons of the year and the infection parameters were significantly different between the years of study. The significant differences in the infection levels of the 2 acanthocephalan species at the 2 sampling sites were surprising as both acanthocephalan species use the same intermediate host, Asellus aquaticus, and the sampling sites were in close proximity and were similar in terms of water quality, host size and invertebrate abundance. Differences in the fish communities of the 2 sampling sites and eel movements rather than interspecific competition are discussed as possible explanations for the differences in the parasite communities of the 2 sampling sites.