Estuarine areas usually suffer significant trace element contamination effects, resulting in significant environmental risks. This is the case of the Paranaguá Estuarine System (PES), located in Southern Brazil, home to one of the largest ports in Latin America and it still boasts of a remarkable biodiversity surrounding by threatened mangrove areas. In this context, this study aimed to assess the quality of sediments concerning metals and metalloid As contamination and comparison to sediment contamination guidelines. In addition, biochemical normalization factors were applied to find out if the sources of the investigated elements were natural or anthropogenic. In 2018, 38 surface sediment samples were sampled seasonally from different PES areas to the determination to metals, metalloid As, and geochemical characteristics. Higher element values analyzed were detected close to the cities of Antonina and Paranaguá and near river mouths, potentially associated with port activities and anthropogenic throughout the surrounding drainage basins. The results revealed concentrations above the Threshold Effect Level (TEL) for Cr, Cu, and metalloid As. The Principal Component Analysis of the analyzed variables showed a strong interaction involving metals/metalloids, organic matter, nutrients, total organic carbon and the fine fraction of sediments. Metals and metalloid As concentrations were lower than in other tropical estuaries, which may indicate water column desorption or aquatic organism absorption, potentially associated to physicochemical water variations or sediment remobilization and resuspension due to dredging activities. The applied geochemical indices indicate low to moderate PES sediment contamination, although some areas presented high values, leading to ecological concerns.