The aim of this research is to analyse and project the effects of changing climate on Lithuanian river runoff and water temperature. Climate change is expected to affect the extremes of the major river indices that impact fundamental ecological processes in river ecosystems. The available runoff and temperature data of rivers from three different hydrological regions of Lithuania were used. HBV software was applied for modelling of hydrological processes in the selected river catchments. The expected future changes of runoff and water temperature were projected according to a new set of scenarios (called representative concentration pathways) presented in the Intergovernmental Panel on Climate Change Fifth Assessment Report. The projected extreme values of runoff (flood and low flow discharges) and water temperatures in the beginning and the end of the 21st century were compared to the ones from the past period. The results showed a decrease of spring flood discharges and summer low flows and an increase of river water temperature at the end of the 21st century. The results are going to be used for an integrated assessment of the impact of climate change on aquatic animal diversity and productivity.