The endoparasitic fauna of Acestrorhynchus lacustris from eight marginal lagoons of the upper and middle São Francisco river basin, Brazil, is recorded here for the first time. For this, a total of 106 specimens of A. lacustris were collected. Eighteen helminth species were found. The taxa recorded were phylum Platyhelminthes: one metacercaria of Clinostomum sp. (Trematoda: Clinostomidae) and plerocercoid larvae of unidentified species (Eucestoda: Proteocephalidae gen. sp.); phylum Acanthocephala: juvenile of Quadrigyrus sp.; and phylum Nematoda: larvae of Brevimulticaecum sp., Contracaecum sp. Type1, Contracaecum sp. Type2, Hysterothylacium sp., Gnathostoma sp., Spiroxys sp., juvenile and adult specimens of Freitascapillaria sp., Paracapillaria piscicola, Capillariidae gen. sp., Procamallanus (Spirocamallanus) hilarii, Procamallanus (S.) inopinatus, Procamallanus (S.) saofranciscencis, Travassosnema travassosi paranaensis, Cystidicoloides fischeri and Spinitectus rodolphiheringi. Proteocephalidae gen. sp., Contracaecum sp. Type1 and Travassosnema t. paranaensis were present in all eight lagoons with high parasitic indexes. Proteocephalidae gen. sp., Brevimulticaecum sp., Gnathostoma sp., Freitascapillaria sp., P. piscicola, Capillariidae gen. sp., Procamallanus (S.) hilarii, C. fischeri and S. rodolphiheringi are new records for A. lacustris. The known geographical distribution of Gnathostoma sp., Freitascapillaria sp., P. piscicola, Capillariidae gen. sp., Procamallanus (S.) hilarii and Travassosnema t. paranaensis has now been extended to the São Francisco river basin.