The distribution of six common metal contaminants (Cd, Cr, Cu, Ni, Pb, Zn) in the bulk (<2 mm) and fine fractions (40% of sand fraction, metal concentrations were up to seven times higher in the fine fraction, implying the necessity for considering sand dilution effect in compositional data analysis. The same samples were also characterized with higher organic matter content (OM) in the fine fraction. Lake environments were characterized by fine-grained sedimentation and the difference between metal concentrations in the bulk and fine fraction was not so expressed. The preparation of samples for the geochemical and compositional data mining should be carried out in accordance with the sedimentological characteristics of the investigated environment. It implies that the insight into geological setting and determination of sedimentological characteristics should be an obligatory part of monitoring/investigating metal contamination in freshwater sediments. For river sediments, the analysis of the fine sediment fraction or correction for sediment lithology are advisable.