The concentration of the major and trace elements in the riverine waters of the Upper Amur basin (Transbaikalia, southeast Siberia) in the Late Holocene (5.5–1.2 kya) was determined by their accumulation in the archaeological shells of the Pearlmussel Margaritifera dahurica (Margaritiferidae, Bivalvia). A positive relationship between the accumulation of elements in the recent shells and their average long-term content in the aquatic environment was revealed. Based on the equations of the relationship between the accumulation of metals in the Pearlmussel shells from archaeological excavations, the content of each element in the aquatic paleoenvironments on the territory of the Upper Amur basin was calculated. We show that the current content of heavy metals in the river waters of this region is significantly increased compared with the same of Late Holocene, which indicates an increase in pollution of the aquatic environment by anthropogenic impact. The empirical relationship between the accumulation of metals in shells and their content in water adequately describes their accumulation in archaeological shells and living mollusks of the same species. The concentrations of the major and trace elements in archaeological shells of Margaritifera and their paleoenvironment may be accepted as background values for the rivers of the Upper Amur basin.