In the Republic of Moldova, the total concentrations of Cu and Zn in surface waters are regulated by the regulation on environmental quality requirements for surface waters, approved by Government Decision no. 890 of 12 November 2013. The purpose of this study is to analyze the dynamics of Cu and Zn in the waters of the Prut River in the territorial limits of the Republic of Moldova, as well as to establish the ratio between the forms of migration (dissolved and suspended) of these metals in recent years. The study of the concentrations and forms of migration of microelements in the dissolved fraction, suspensions, sediments and aquatic organisms is an imperative for science, especially in the XXI century, when anthropogenic pressure on the environment increasing. Сu and Zn can penetrate surface waters from both natural and anthropogenic sources. In the Republic of Moldova the main source of water pollution with Cu and Zn is agricultural activity, given the presence of these metals in various chemicals used. The dynamics of Cu and Zn concentrations in recent years, compared to the '80s and' 90s of the last century, show a decreasing trend. The migration capacity of microelements in surface waters and their forms of migration are conditioned both by the properties of the elements themselves and the physico-chemical peculiarities of the environment, by the redox conditions, the size of pH, temperature, the presence of agents of complexation, of suspended substances, of the vital activity of hydrobionts, etc. The study of the correlation between suspended and dissolved forms of migration of microelements in river waters is important in assessing their influence on living systems and is of great importance in hydrogeochemical research. Cu and Zn are essential nutrients in the development of living organisms, but can represent toxic effects at higher concentrations. Considerable concentrations of these metals, including other microelements in surface waters can make water unsuitable for use as a drinking source, for food preparation, recreation, household use, irrigation, in industry, etc. And as a result they can have negative effects on the health of both humans and aquatic organisms, but even worse can lead to complete disruption of the normal functioning of the ecosystem. In this context, it is necessary to constantly monitoring the concentrations of metals, including Cu and Zn in aquatic ecosystems, in order to prevent pollution as well as timely intervention.