The impacts of climate change are significant on both surface and groundwater resources. However, little attention has been given to the effect of climate change on groundwater resources. Therefore, the present study is concerned with the effect of climate change on groundwater recharge and base flow in Muda River Basin, Malaysia. The model simulations were based on 55 years of historical rainfall and runoff data (1960-2015) while climate change scenarios were run for 50 years from 2016–2050 using different downscaled Global Climate Model projections. The future climate variables were obtained from five GCMs projection were downscaled. These GCMs include i) CanESM2 from Canadian Centre for Climate Modelling and Analysis, ii) GFDL-CM3 from Geophysical Fluid Dynamic Laboratory NOAA, iii) HadGEM2 from UK Met Office, iv) IPSL-CM5 from Institut Pierre-Simon Laplace and v) MIROC5 from Japan Agency for Marine-Earth Science and Technology Frontier Research Centre for Global Change. For each GCM downscaled projection, results for two representative concentration pathways (RCPs) have been produced, namely: RCP 4.5 and RCP 8.5. These pathways describe possible future climates depending on how much greenhouse gases are emitted in the years to come. The results indicated the average annual runoff resulting from each GCM, three future possible climate scenarios were determined as Dry (CanESM RCP4.5), Intermediate (HadGEM2 RCP8.5) and Dry (MIROC5 RCP4.5) The results of this study would help policymakers, scientists, government officials and local stakeholders in planning and management of the surface and groundwater resources in the Malaysia regions.