The study presents the results of Cu, Pb, Zn, Mn and Fe determination in the samples of bottom sediments collected from the Oder and Warta rivers. The sequential extraction of metals in the samples of bottom sediments was performed after introducing the modification of the extraction scheme suggested by Tessier et al. (Anal Chem 51(7):844-851, 1979). The extraction times of particular stages were optimised. The fifth stage was altered by introducing the new methods of performing extraction. The samples of bottom sediments submitted the following granulometric analyses: dry, wet and wet with (HMP) dispersing reagent. Seven granulometric fractions with the following grain sizes were isolated: [2.0, 2.0-1.0, 1.0-0.5, 0.5-0.25, 0.25-0.1, 0.1-0.063 and \0.063 mm. The sequential extraction of particular granulometric fractions was performed. The concentration of metals variability was analysed depending on the method of sample preparation for the chemical analysis, granulometric fraction of sediments subjected to the analysis, extraction conditions and the site of samples collection. The lack of linearity between the metal concentration and the size of granulometric fraction was observed. The highest concentrations of metals were observed in fractions [2.0, 2.0-1.0 and 0.1-0.063 and \0.063 mm while the lowest concentrations occurred in fractions 1.0-0.5, 0.5-0.25, and 0.25-0.1 mm. The atomic absorption spectrometry with flame atomisation (F-AAS) was used for the determination of the investigated elements.