The paper presents an overview of the results of multiannual investigations of the dynamics of migration of several metals in the ecosystems of the Dniester and Prut rivers – the main water courses of the Republic of Moldova. The dynamics of metals in water, suspensions, silts, aquatic plants, planktonic and benthic invertebrates, fish at different stages of development (eggs-larvae, fry, mature fish) was investigated depending on abiotic factors and under the influence of human activity. The fragmentation of the Dniester River, through the construction of several dams, and the operation of the Dniester Hydropower Complex have reduced the processes of sedimentation and self-cleaning in the river, which has reflected on the migration and circuit of metals, causing an imbalance of the native processes of metal migration, characteristic for the river ecosystems of the studied region. The impact of metals on the processes of formation of primary production and destruction of organic matter in aquatic ecosystems and on the development of fish, especially at the early stages of ontogenesis, was identified. The level of accumulation of metals in aquatic plants, planktonic, benthic invertebrates and fish is a reflection of the metal content in the aquatic environment, but also depends on the biological properties of the hydrobionts, and the overall ecological status of the aquatic ecosystem. Synergistic, additive and antagonistic interactions between different metals have been recorded. The identified regularities of the migration and accumulation of metals in the “water-solid suspensions-silts-hydrobionts” system can be used in monitoring and evaluating the functioning of aquatic ecosystems.