The occurrence, distribution, and the total mass of polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) were studied in surficial sediments of the Paranaguá Estuarine System (PES), a subtropical estuary in Southern Atlantic. Altogether, concentrations and inventories of contaminants ranged from <0.06 to 4.78 ng g−1 and < 0.13 to 10.47 ng cm−2, respectively. OCPs presented the higher total mass (10.85 kg) and a decreasing trend from the inner estuary towards the adjoining shallow shelf. The occurrence of PCBs was restricted to sites nearby urban and industrial areas, which accumulated ~80% of the total mass of PCBs. Although the level of contamination is low, the results refer to recent years, which mean that the actual values could be greater if sediments from periods of higher usage were analyzed. This study provides the first estimates of POPs (persistent organic pollutants) total mass in the PES, contributing to data for the Southern American inventories.