The article focuses on studying the total content and chemical fractions of heavy metals (Fe, Mn, Co, Cr, Cu, Ni, Pb, V, Zn) in sediments of two lakes on Samoylov Island in the Lena delta. The lakes differ in genesis and hydrological conditions. Geochemical data for the study area were summarized. We used the sequential extraction procedure to research the roles of different sediment components in the accumulation of microelements. ICP AES was the method for all the chemical analyses. The results reveal a quite homogeneous vertical distribution of heavy metals in cores from the two lakes over the entire period of their existence (ca. 3 Ka according to radiocarbon dating). The average concentrations of the heavy metals were comparable to their content in sediments from other lakes, as well in the island soils. Analysis of the chemical fractions of the heavy metals showed that the elements were mainly stored in stable forms (bound to the crystal lattice of minerals). However, humic matter plays a significant role in binding the cations of all the metals to stable complex compounds. Cu, Pb and Zn had the most organophilic properties in the two lakes. It was noted that a significant proportion of Ni, Cr, Zn and Cu was bonded with Fe and Mn oxides. Cr, Cu, Zn and Mn were found in potentially bioavailable forms. The most mobile elements were Mn and Zn. There is a high risk of secondary water pollution with these metals.