Climate changes may generate significant impacts in hydrological cycle. It is important to recognize modifications in green water (water stored in soil and then consumed by vegetation) and blue water (water that flows in rivers, lakes, wetlands and shallow aquifers) availability in consequence of climate change modifications. In this context, mathematical modelling is used to simulate the effect of climate change scenarios in hydrological processes in watersheds. Therefore, this paper aims to assess the impacts of climate change in blue and green water in Apucaraninha River watershed (504km²), Southern Brazil, considering the climate scenario A2 (pessimistic about greenhouse gases emissions) and climate scenario B2 (optimistic about greenhouse gases emissions), developed by IPCC. SWAT model (Soil and Water Assessment Tool) was calibrated and validated using daily streamflow from 1987 to 2012. Climate scenarios A2 and B2 were used to simulate the hydrological conditions for the period 2071-2100. The model presented satisfactory fit compared to the observed data allowing the simulation of the current hydrological conditions, therefore permitting the simulation of future climate change impacts in green and blue water. We found that despite the increase in potential evapotranspiration of 19% and 12% for A2 and B2 scenario respectively, caused by the increase in temperature, the reduction in rainfall amount (19% for A2 and 23% for B2) induced to a reduction in actual evapotranspiration (16% for A2 and 33% for B2), which correspond to green water, and a reduction of 21% for A2 scenario and 14% for B2 scenario in blue water availability.