Determining heavy metal background concentrations in soils is fundamental in order to support the monitoring of potentially contaminated areas. This is particularly important to areas submitted to high environmental impact where an intensive and local monitoring is required. To this end, the aim of this study was to establish background concentrations and quality reference values (QRVs) for the heavy metals Cd, Cr, Cu, Fe, Mn, Ni, Pb, Zn, As, and Hg in an environmentally impacted watershed from Brazil. Geochemical associations among Fe, Mn, and trace elements were also assessed to provide an alternative tool for establishing background concentrations. A total of one hundred and four samples comprised twenty-six composite soil samples from areas of native forest or minimal anthropic influence. Samples were digested (USEPA method 3051A), and the metals were determined by ICP-OES, except for As and Hg measured by atomic absorption spectrophotometer. Background concentrations of heavy metals in soils had the following decreasing order: Fe > Mn > Zn > Cr > Pb > Ni > Cu > As > Cd > Hg. These values were usually lower than those observed in the international and national literature. The QRVs for Ipojuca watershed followed the order (mg kg −1) Fe (13,020.40) > Mn (91.80) > Zn (30.12) > Cr (15.00) > Pb (13.12) > Cu (3.53) > Ni (3.30) > As (0.51) > Cd (0.08) > Hg (0.04). Significant correlation among Fe, Mn, and heavy metals shows that solubilization by the method 3051A provides a reasonable estimate for predicting background concentrations for Cd, Cr, and Cu as well as Zn, Cr, Cu, and Ni.