The concentrations of As, Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn (TE) in four juvenile fishes (Acestrorhynchus pantaneiro, Salminus brasiliensis, Brycon orbignyanus, and Megaleporinus obtusidens) and associated sediment water from the Lower Paraná River were measured. For muscle, gills, and liver fishes, the TE accumulation in the muscle, gills, and liver was evaluated. The TE concentration was measured by quadrupolar inductively coupled plasma mass spectrometry (Q-ICP-MS). Cadmium (0.25 ± 0.07 μg L-1), Cu (3.00 ± 1.44 μg L-1), Fe (612 ± 69 μg L-1), and Pb (1.92 ± 1.20 μg L-1) in water and As (4.1-6.9 μg g-1), Cr (20.1-31.4 μg g-1), Cu (10.7-19.2 μg g-1), Mn (351.3-482.2 μg g-1), and Ni (24.5 ± 10.9 μg g-1) in sediments exceeded the guide values for the conservation of aquatic life. In general, muscle of omnivorous species (B. orbignyanus and M. obtusidens) showed higher values of elements than those of carnivorous species (A. pantaneiro and S. brasiliensis). However, TE concentrations varied with fish species and organs. Independently of the examined species, the highest concentrations of Cr and Pb were in the muscle and gills, respectively. Cadmium, Cu, and Fe concentrations were higher in the liver than in gills and muscle in all four fish species. These results were consistent with the tissue selectivity index analyzed. For the four species, major essential elements showed the highest accumulation. However, the accumulation of toxic elements in omnivorous fish was higher than in carnivorous fish. The individual pollution load index indicated that sediment was very polluted with As and Pb, but based on the combined ecological indexes, low elemental sediment pollution in the Espinillo Lake was revealed. © 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.