ABSTRACT The parasitic fauna of reptiles is considered understudied compared to that of other vertebrates and is even less well known than the parasitic fauna of chelonians. Yet parasites are considered one of the main controllers of host populations because they can strongly impact population structure and species diversity. The objective of the present study was to identify the helminth fauna infecting freshwater turtles Phrynops geoffroanus and Mesoclemmys tuberculata, to evaluate the effects of host features (body mass and sex) and seasonality (dry and rainy seasons) on the abundance of parasites, and to compare infection rates in each host species between different biomes (Caatinga and Atlantic Forest) in an area of Northeastern Brazil. We found seven species of helminths that belong to Nematoda (Physaloptera sp., Serpinema amazonicus, Serpinema monospiculatus and Spiroxys figueiredoi), Cestoda (unidentified specimen), Digenea (Echinostomatidae) and Monogenea (Polystomoides brasiliensis). For both freshwater turtle species, we did not find a significant difference in the abundance of helminths related to the maximum carapace length, body mass or host sex; however, males had higher prevalence than females, while females presented greater abundance when infected. We observed significant differences in the infection levels between biomes and between seasons (dry and rainy), where the Atlantic Forest specimens showed higher infection rates compared to the Caatinga and the highest rates occurred in the dry season. The main parasitological parameters observed in P. geoffroanus and M. tuberculata showed that the studied biomes directly influenced the levels of parasitic infection. Variations in habitat characteristics can directly influence patterns of helminth diversity and abundance, and interactions between these characteristics can generate differences in parasitism rates of the same host species in different environments.