This study characterized and mapped the spatial variability patterns of seven topsoil heavy metals (Cr, Ni, Pb, Cu, Zn, Hg and Cd) within the Ebro river basin (9.3 million ha) by Multivariate Factorial Kriging. The variograms and cross-variograms of heavy metal concentrations showed the presence of multiscale variation that was modeled using three variogram models with ranges of 20km (short-range), 100km (medium-range) and 225km (long-range). Our results indicate that the heavy metal concentration is influenced by bedrock composition and dynamics at all the spatial scales, while human activities have a notorious effect only at the short- and medium-range scale of variation. Sources of Cu, Pb and Zn (and secondary Cd) are associated with agricultural practices (at the short-range scale of variation), whereas Hg variation at the short- and medium-range scale of variation is related to atmospheric deposition.