In the conditions of environment instability and pollution, and climate change, the research and identification of chemical compound patterns of accumulation, their optimal and toxic limits, as well as assessment of the influence of hydrochemical and hydrobiological parameter fluctuation on fish contribute significantly to the solving of problems of fundamental character. These are related to the determination of hydrobiont tolerance, assessment of chemical element circuit, migration and flow in food chains, aiming to elaborate and implement the biotechnologies in order to restore and increase the fishery productivity, fish product quality, and also the methodology of aquatic ecosystem monitoring and sustainable exploitation. During the last decades a range of investigations have been carried out on accumulation, migration and influence of microelements – metals on the production-destruction processes in aquatic ecosystems and cyprinids and percids development (Zubcov E., 2000; Zubcov N., 2011). Some procedures of microelement application as stimulators of fish resistance and for improvement of trophic base in aquatic ecosystems used for fish culture were worked out (Zubcov et al., 1998; Zubcov et al., 2011). The obvious negative changes of the Dniester and Prut river ecosystems are caused by anthropogenic impact on their hydrological parameters. The situation is aggravated by the climate change, which influenced the diversity and bioproductivity of above mentioned rivers, they being, particularly, cross-border water streams. It is absolutely necessary an international collaboration between researchers and specialists in order to diminish the negative consequences, restore the fish diversity, increase the aquaculture productivity and exploit the aquatic resources in a sustainable manner. These investigations should be guided towards the large scale implementation of new methodologies and biotechnologies, designed for fish diversity restoration, including the breeding of rare fish species by application of their artificial reproduction, usage of biological stimulators of fish resistance, fish reintroduction in river and lake ecosystems by their stoking with larvae and fry, taking in account the physical and geographical conditions and the state of aquatic environment.