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Understanding the geological evolution of the Pelotas and Punta del Este basins is crucial for a more comprehensive insight into the South American passive margin. Nevertheless, despite their significant geological value, these basins have hitherto been lacking in geochemical studies. Addressing this knowledge gap, we carried out new whole-rock geochemistry and, for the first time in these basins, zircon U-Pb provenance studies. Our geochemical analysis offered a robust evaluation of the overall provenance and maturity of the sediments that fed the basins, while the new detrital zircon studies allowed for precise identification of the source areas. The detrital zircon points to multiple sources, with main provenance related to grains accretioned during the Brazilian-Pan-African tectonic cycle and significative changes from the Cretaceous to nowadays. Additionally, the detrital zircon analyses offered an enhanced understanding of the basin basement and the influence of littoral drift and bottom currents on the sedimentation of the Punta del Este and Pelotas basins. In conclusion, this investigation demonstrated the importance of geochemical and provenance studies for a better understanding of the geological history and hydrocarbon potential of the Pelotas and Punta del Este basins.