Aquatic ecosystems are particularly vulnerable to anthropogenic activity and climate change. The changes in flow regimes in Lithuanian lowland rivers due to the operation of hydropower plants (HPPs) and the impact of altered flow on some fish species have already been studied. The impact of climate change on future natural river runoff and the structure of fish assemblages was also investigated. However, it is still unknown how the combined effect of climate change and flow regulation related to hydropower generation may affect fish assemblages in the downstream river reaches below the Lithuanian HPPs. In this study, the physical habitat modelling system MesoHABSIM was used to simulate spatial and temporal changes in aquatic habitats availability for different fish species under the influence of HPP at different climate change scenarios. Changes in the available habitat were assessed for common fish species in four HPP-affected rivers representing different hydrological regions of Lithuania. The modelling results showed that the operation of HPP under climate change conditions in most rivers could be beneficial for small benthic fish species such as gudgeon Gobio gobio and stone loach Barbatula barbatula. Meanwhile, for larger fish species (e.g., chub Squalius cephalus and vimba Vimba vimba) the alteration in the temporal availability of suitable habitat was relatively higher.