An extensive survey of macroparasites in 320 European eel Anguilla anguilla (Linnaeus, 1758) was conducted in two brackish lagoons and eleven freshwater localities in the Mediterranean island of Corsica (France) between spring 2021 and winter 2021–2022. It resulted in the identification of nineteen parasites: two Monogea, four Digenea, one Copepoda, four Acanthocephala, three Cestoda, and five Nematoda, including the first geographical records, as Corsican freshwater sites were studied for the first time. The silvering stage was determined, and the eels were aged through otolithometry to compare parasite communities. Classic parasitology indices, a multivariate analysis, and an analysis of indicator values (IndVal) showed clear preferences towards the host’s habitat and salinity. Seasonal variations were shown for several parasites. A dataset from the same two coastal lagoons was used to study the changes in the parasite communities over the last decade, and this showed an increase in the prevalence and abundance of three invasive helminth species: the Monogenea Pseudodactylogyrus bini (Kikuchi, 1929), Pseudodactylogyrus anguillae (Yin and Sproston, 1948 and Gusev, 1965), and the Nematoda Anguillicola crassus (Kuwahara, Niimi, and Itagaki, 1974). These pathogenic parasites were found in all sampled localities, except for the two Monogenea in the polyhaline-to-euhaline Urbino lagoon. It is thus advised that future management measures take into account the environmental preferences of the most concerning parasites.