Water availability restrictions are already a reality in several countries. This issue is likely to worsen due to climate change, predicted for the upcoming decades. This study aims to estimate the impacts of climate change on groundwater system in the Guarani Aquifer outcrop zone. Global Climate Models (GCM) outputs were used as inputs to a water balance model, which produced recharge estimates for the groundwater model. Recharge was estimated across different land use types considering a control period from 2004 to 2014, and a future period from 2081 to 2099. Major changes in monthly rainfall means are expected to take place in dry seasons. Most of the analysed scenarios predict increase of more than 2 ºC in monthly mean temperatures. Comparing the control and future runs, our results showed a mean recharge change among scenarios that ranged from ~-80 to ~+60%, depending on the land use type. As a result of such decrease in recharge rates, the response given by the groundwater model indicates a lowering of the water table under most scenarios.