Water scarcity issues in the Johor River Basin (JRB) could affect the populations of Malaysia and Singapore. This study provides an overview of future hydro-meteorological droughts using climate projections from an ensemble of four Coordinated Regional Climate Downscaling Experiments – Southeast Asia (CORDEX-SEA) domain outputs under the Representative Concentration Pathway (RCP) 4.5 and 8.5 scenarios for the 2021–2050 and 2071–2100 periods. The climate projections were bias corrected using the quantile mapping approach before being incorporated into the Soil and Water Assessment Tool (SWAT) hydrological model. The Standardized Precipitation Index (SPI) and Standardized Streamflow Index (SSI) were used to examine the meteorological and hydrological droughts, respectively. Overall, future annual precipitation, streamflow, and maximum and minimum temperatures are projected to change by about −44.2 to 24.3%, −88.7 to 42.2%, 0.8 to 3.7ºC and 0.7 to 4.7ºC, respectively. The results show that the JRB is likely to receive more frequent meteorological droughts in the future.