Conservation of biological diversity in ecosystems, species, populations and genes is one of the main concerns of mankind in the third millennium. The problem is that with the advancement of technological progress and the intensive use of natural resources, the anthropogenic impact on biological diversity has considerably increased, significantly reducing the number of species and varieties of living organisms that populate the Earth. Assessing the impact of biochemical processes at the sediment-water interface in aquatic ecosystems in the Biosphere Reserve ,,Prutul de Jos” on biodiversity in the context of climate change is important in that it includes biochemical research at the sediment-water interface, including the establishment of properties surface area and influence of the organic-mineral complex, amorphous phase, interstratular material of clay minerals, determination of mineralogical features, changes in the cation exchange complex, spatial dynamics of heavy metals in sediments, their chemical partition in particle constituents and their mobility in aquatic ecosystems, such as and evaluation of the complex influence of abiotic factors on water quality, establishing the kinetic characteristics of biochemical transformations of nitrogen in aquatic ecosystems, consumption of dissolved oxygen in water, self-purification capacity of the aquatic ecosystem, use of the model for ru biochemical simulations and for practical purposes, for modeling and forecasting ecological crisis situations in the water basins of the Biosphere Reserve ,,Prutul de Jos” and assessing the impact of these processes on the biodiversity of the aquatic ecosystem as a whole. Climate change, changes in water circulation, intensification of water evaporation processes, eutrophication of water basins are becoming a concern for the environment and human health. That is why it is important to detect, monitor and evaluate the impact of different metabolites eliminated in the aquatic environment following the processes at the sediment-water interface and the impact on aquatic flora and fauna. The object of study is the ,,Prutul de Jos” Biosphere Reserve (Republic of Moldova) located in the southwest part of the country. This biosphere reserve includes the Prut River and several floodplains. Two thirds of the area is occupied by Lake Beleu. A wetland stretches along the Prut River, covering a mosaic of water ecosystems, meadows and forests. The reservation was established by Law no. 132/2018 on the founding of the ,,Prutul de Jos” Biosphere Reserve, and was included in the UNESCO World Network of Biosphere Reserves [1]. The aquatic ecosystems from the ,,Prutul de Jos” Biosphere Reserve have an impact on the Danube - Black Sea river basin . This study addresses and integrates existing recommendations in a series of European Directives on water and biodiversity, and obtained results contribute to the scientific substantiation of the development of recommendations for the harmonization of the methods used and the improvement of water management exploited on the national territories of the Republic of Moldova and Romania.