The overall objective of this study is to estimate, detect and specify the main sources of variance which affect the contents of the different elements in overbank sediments across Spain. These sources of variance were assessed and compared by means of a series of analyses of variance (ANOVAs), by regarding two parameters: their significance and their contribution to the total variance. Overbank sediments, sampled in erosion banks, were studied in several locations, in basins which drain different types of geological backgrounds and land uses (urban, mining, agricultural or pristine) across the Iberian Peninsula. Forty-eight elements (mostly in the < 63 μm fraction) were analysed by ICP-OES, ICP-MS and INAA. After an isometric log ratio (ilr) transformation of the data, three ANOVA analyses were performed considering three perspectives: (1) local scale, (2) regional scale: within-profile perspective and (3) regional scale: inter-profile perspective. On a local scale, it was observed that the variability of rare earth elements (REE) depends mostly on the grain size and that heavy metals are also influenced by depth. In the analysis carried out on a regional scale, from a within-profile perspective, depth and duplicates do not influence significantly the variability of the element contents. Finally, from an inter-profile perspective, the selected sources of variance were land use and provenance, whose significance is the highest. While grain size and the selection of depth are of crucial importance in the final results, on local studies, land use and provenance are the ones that influence the most the composition of sediments in regional studies.