Hypostomus commersoni is a freshwater fish, native to the Paraná River basin, which plays an important role in trophic networks of this system. This study aimed at analyzing the structure of the endohelminth community of H. commersoni from two shallow lagoons in the municipality of Santa Fe, Argentina. In the 51 hosts analyzed, 2103 helminths were found. Hosts from Belgrano Park lagoon were infested with Genarchella genarchella, Saccocoelioides nanii, Raphidascaris (Sprentascaris) sp., and Gorytocephalus elongorchi. Hosts from the Western Urban Nature Reserve lagoon were infested with Thometrema magnifica, Procamallanus (Procamallanus) annipetterae, Raphidascaris (Sprentascaris) sp., Gorytocephalus elongorchi, and Proteocephalidae spp. In both host populations, the prevalence of some parasites was high, and species richness and diversity of component communities were low. The distribution pattern of helminth was aggregated in all cases. No correlation was found between the length of the host and the richness and abundance of endoparasites. The total number of parasites and the specific richness per host in both lagoons did not differ significantly. The findings on G. genarchella, P. (P.) annipetterae, G. elongorchi, and Proteocephalidae spp. were the first records in his host