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Trace metal background levels determination is essential for the proper assessment of the contamination status of a region. This study aims to integrate geochemical and statistical methods for the reliable determination of background levels, applying it to the sediments of the Paranaguá Estuarine System (PES), a large subtropical estuarine system of international importance since it is considered a World Heritage Site and Biosphere Reserve and it harbors the main South American grain shipping port. Prediction Interval (PI) was applied as a chemometric tool to evaluate metal enrichment without a reference level and assess a regional background. Moreover, the sources and concentrations of major and trace elements were assessed in surface sediments from 135 sampling sites located in the Paranaguá Estuarine System (PES). PES surface sediment elements concentrations may be considered lower than those found in other anthropized environments indicating no significant contamination for most of the studied elements (Cr, Cu, Ni, Pb and Zn). The levels of As in the PES may be related to the geochemical characteristics of the adjacent drainage basin and the occurrence of phosphate rocks, which contain As in their composition. However, As was also influenced by anthropogenic inputs either from agricultural activities or fertilizer industries working with mining phosphate in the region. KeywordsMajor and trace elements • World Heritage Listed area • Background levels • Chemometric tool