Summary The aim of the study is to estimate the role of sediment components in the accumulation of microelements in lakes of the permafrost-affected area (the Lena Delta, northern Siberia). A fractional analysis of several trace elements (V, Cr, Co, Ni, Cu, Zn, Sn, and Pb) was conducted. Samples were collected from 10 lakes during the summer period of the “LENA 2019” expedition. The content of the chemical elements in the sediments was measured with the ICP-MS instrument. The results of the work show a relatively homogeneous distribution of the acid-soluble forms of the metals in sediments from different lakes. The content of trace elements in all the lakes studied is determined by natural (lithogenic) sources. Stable minerals inherited from the rocks play a crucial role in the sediment formation. Most of the elements are predominantly fixed in stable mineral and organometallic fractions. However, for V, Co, and Cr a high level of geochemical mobility was identified in some of the lakes. The metals of soluble complexes are capable of migrating from the sediments to the water due to physical and chemical changes in the aquatic environment. Furthermore, the organic substances and the Fe/Mn hydroxides of the sediments have a low potential ability to bind the metals into stable compounds.