The Papan and Naiman reservoirs are artificial reservoirs created to supply drinking water to the city of Osh and the settlements of the Nookat and Aravan regions. The object of study of ecology, including aquatic ecology (hydroecology, hydrobiology), is an aquatic ecosystem, which is an interconnected system of living organisms and their natural environment (water, sediments and adjacent land), in which substances and energy are formed, and there is a cyclic exchange of minerals and organic matter. Aquatic ecosystems are a complex type of artificially created reservoirs with a regulated water regime, as a result of which the level and speed of flow change, thereby determining the nature of the hydrobiological regime. The process of formation of a reservoir ecosystem depends on its specific conditions, initial biological resources, water exchange, anthropogenic loads, etc. Effective and environmentally safe use of water and biological resources of reservoirs can only be realized on the basis of a deep and comprehensive study of the structure and functioning of their ecosystems. The object of the study was the taxonomic composition of the phytoplankton of the Papan and Naiman reservoirs, located in the south of Kyrgyzstan. The relevance of the study is determined by the importance of these reservoirs in the national economy and in providing the population with clean water.