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The research was carried out as part of the preparation "Water Resources" section of the 4th National Communication of the Kyrgyz Republic to the UNFCCC. The article presents extensive information on the current state and changes over a long period of observations of water resources, climate and glaciation in Kyrgyzstan (Syr-Darya and Amu-Darya river basins). The representative rivers were selected as the main objects, which are transboundary between Kyrgyzstan, Uzbekistan, Kazakhstan and Tajikistan. The study aims to assess the inter-annual and intra-annual dynamics of the flow of the rivers for the period from 2020 to 2080, based on the climate projections CMIP5 (RCP4.5 and RCP8.5) and CMIP6 (SSP2-4.5 and SSP5-8.5) (IPCC WG II Report, 2022). The hydrological modeling method in the HBV light and HBV EHT models and the inertial mean annual flow change method were used to estimate changes in water resources. On the rivers of the northern part of the Fergana Valley, the average annual runoff is expected to increase by 1-19%, in the Amudarya river basin (Kyzyl-Suu river) - by 27-64% of the values for 2006-2019. In the Naryn river, water discharge for this period will remain within the current values for 2006-2019. The method of inertial change in the average annual runoff showed an increase in runoff for 2030 and 2040 for all the studied catchment areas by 6-19% of the current values for 2006-2020T. he results of the study are intended for decision-makers on the rational use and long-term planning of water resources under climate change. [ABSTRACT FROM AUTHOR]