Hydropower (potential and kinetic energy) is one of the most important renewable energy sources in the world. This energy is directly dependent on water resources and the hydrological cycle. Ongoing climate changes are likely to influence the availability/amount of this energy resource. The present study explores the relationship between climate changes and river runoff, projects future runoff in both gauged and ungauged river catchments, and then assesses how these alterations may affect the future hydropower resources in Lithuania. Runoff projections of the gauged rivers were evaluated applying Swedish Department of Climate hydrological model, and runoff of ungauged river catchments were estimated by created isoline maps of specific runoff. According to an ensemble of three climate models and two Representative Concentration Pathway scenarios, runoff and hydroelectric energy projections were evaluated for two future periods (2021–2040, 2081–2100). The results demonstrated a decrease in future river runoff. Especially significant changes are expected according to the most pessimistic RCP8.5 scenario at the end of the century. The projected changes are likely to bring a negative effect on hydropower production in the country. These findings could help understand what kind of benefits and challenges water resource managers may face in the future.