Abstract Catfish Genidens barbus is a commercially fished species from the south-western Atlantic Ocean. Overfishing of this species during the last few years has caused a collapse of fisheries and in turn has led to a ban of its exploitation. In order to identify the migratory patterns of this species in four migration corridors from South America, we determined the Sr:Ca and Ba:Ca ratios in otoliths, by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICPMS). Sr:Ca and Ba:Ca ratios range between 0.90 and 9.83 mmol/mol (mean ± standard deviation: 3.86 ± 1.05 mmol/mol) and between 0.00013 and 0.10 mmol/mol (mean ± SD: 0.0094 ± 0.0160 mmol/mol), respectively. Three types of amphidromous and cyclical (annual) patterns that include the use of freshwater, estuarine and marine environments are detected. Resident freshwater fish (6.5%) are found only in Patos Lagoon. Depending on the study site, between 18 and 45% of the analyzed fish population were spawned in freshwater, while the rest were spawned in estuarine waters. The change-point analysis shows a positive correlation between changes in the transects of Sr:Ca and Ba:Ca ratios (r = 0.63, p = 0.0001), whereas the Kruskal-Wallis test shows no significant differences in the number of changes in transects of the Sr:Ca ratio between sampling sites (H = 2.1, p = 0.53). Only for Patos Lagoon the analyses show a significantly higher number of changes for the Ba:Ca ratio (H = 9.1, p = 0.03). The data indicate that the average number of movements among environments is similar between the four corridors. The number of changes of the Ba:Ca ratio appears to be higher and more variable in relation to the Sr:Ca ratio, indicating that the former could be more sensitive to environmental changes. In conclusion, this work describes for the first time, annual amphidromous migrations and dependence on freshwater for different fluvial-marine systems. The understanding of the habitat use will help design species and estuarine-specific management actions with the ultimate goal of recovering fisheries.