Extensive Cu- and Zn-soil geochemical data in the Albernoa/Entradas–S. Domingos region (NE border of the Iberian Pyrite Belt, South Portuguese Zone) were examined to separate anomalies from background using the concentration–area fractal model. Distribution patterns of Cu and Zn concentrations in soil are primarily influenced by bedrock. The regional threshold values of Cu- and Zn-soil contents over metasedimentary sequences are 20–25 and 20–60 ppm, respectively, becoming 30–50 and 20–90 ppm, respectively, when metavolcanic rocks are present. The first-order threshold values for Cu are 80–90 ppm in soils over metasediments and 70–80 ppm in soils over sequences bearing metavolcanics. For Zn, the first-order threshold values are 40–80 and 90–100 ppm in soils over metasediments and metavolcanic rocks, respectively. Metasediments and metavolcanics comprising significant sulphide disseminations are outlined by Cu- and Zn-soil values above 100 and 300 ppm in soil, respectively. On the basis of these results, Alvares and Albernoa/Entradas areas emerge as the first priority targets for exploration. The observed non-coincidence of Cu- and Zn-soil anomalies in soil in the area could reflect difference in element dispersion during weathering, they mostly indicate distinct metal sources related to the original composition of different rock types or to chemical changes developed during Variscan deformation/re-crystallization path. The established regional baseline data can be used as reference for environmental studies.