Alterations of abiotic factors (e.g., river water temperature and discharge) will definitely affect the fundamental processes of aquatic ecosystems. The purpose of this study was to examine the impact of climate change on the structure of fish assemblages in fast-flowing rivers belonging to the catchment of the major Eastern European river, the Nemunas. Five catchments of semi-natural rivers were selected for the study. Projections of abiotic factors were developed for the near (2016-2035) and far future (2081-2100) periods, according to four RCP scenarios and three climate models using the HBV hydrological modelling tool. Fish metric projections were developed based on a multiple regression using spatial data. No significant changes in projections of abiotic and biotic variables are generally expected in the near future. In the far future period, the abiotic factors are projected to change significantly, i.e., river water temperature is going to increase by 4.0-5.1 °C, and river discharge is projected to decrease by 16.7-40.6%, according to RCP8.5. By the end of century, the relative abundance of stenothermal fish is projected to decline from 24 to 51% in the reference period to 0-20% under RCP8.5. Eurythermal fish should benefit from climate change, and their abundance is likely to increase from 16 to 38% in the reference period to 38-65% under RCP8.5. Future alterations of river water temperature will have significantly more influence on the abundance of the analysed fish assemblages than river discharge.