Peats and marsh waters of the peat bog eutrophic ecosystem (Tomsk region) for the content of trace elements have been studied. The peat deposit is composed of lowland peats of grass type predominantly. The deposit average depth is about 3 meters. Samples of several observation points, which differ in botanical composition and hydrothermal conditions of occurrence were analyzed. The concentration of biogenic (Zn, Co, Cr), alkaline (Rb, Cs), alkaline earth (Sr, Ba) and rare earth (Hf, La) metals in peat and marsh waters has been determined by the method of neutron activation analysis. It was shown that the amount of various elements in peat is determined by regional characteristics and botanical composition. From comparative elements concentration analysis, it has been found that concentration of metals varies identically depending on the depth of the peat bog, which indicates typical conditions for the accumulation of these elements. As a result of the research was founded high content of the Ba and Sr in peats of all observation points. It has been established that the peat of native section 3 is enriched with all studied metals Zn, Cr, Sr, Ba in comparison with peats of the first and the second observation points. Besides, under the conditions of this ecosystem cobalt, rubidium and lanthanum were accumulated in peats. The average concentration of trace elements in the studied peat bog ecosystem is comparable to the average values of this region. We have found that samples of marsh water are enriched with the biogenic zinc. Among rare metals, such elements as strontium and barium are the most abundant in marsh water, what correlates with the largest content of Zn, Sr and Ba in the studied peats. Light Rb and Sr ions transfer from peat to swamp waters in greater amount than heavier Cs and Ba ions. Strontium enters and migrates intensively to the swamp waters of all three observation points.