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Uncertainties of runoff projections arise from different sources of origin, such as climate scenarios (RCPs), global climate models (GCMs) and statistical downscaling (SD) methods. Assessment of uncertainties related to the mentioned sources was carried out for selected rivers of Lithuania (Minija, Nevėžis and Šventoji). These rivers reflect conditions of different hydrological regions (western, central and southeastern). Using HBV software, hydrological models were created for river runoff projections in the near (2021-2040) and far (2081-2100) future. The runoff projections according to three RCP scenarios, three GCMs and three SD methods were created. In the Western hydrological region represented by the Minija River, the GCMs were the most dominant uncertainty source (41.0-44.5%) in the runoff projections. Meanwhile, uncertainties of runoff projections from central (Nevėžis River) and southeastern (Šventoji River) regions of Lithuania were related to SD methods and the range of uncertainties fluctuates from 39.4% to 60.9%. In western Lithuania, the main source of rivers' supply is precipitation, where projections highly depend on selected GCMs. The rivers from central and southeastern regions are more sensitive to the SD methods, which not always precisely adjust the meteorological variables from a large grid cell of GCM into catchment scale. [ABSTRACT FROM AUTHOR]