The impact of climate change and uncertainty of climate projections from general circulation models (GCMs) from phase 5 of the Coupled Model Intercomparison Project (CMIP5) on streamflow in the Johor River Basin, Malaysia was assessed. Eighteen GCMs were evaluated, and the six that adequately simulated historical climate were selected for an ensemble of GCMs under three Representative Concentration Pathways (RCPs; 2.6 (low emissions), 4.5 (moderate emissions) and 8.5 (high emissions)) for three future time periods (2020s, 2050s and 2080s) as inputs into the Soil and Water Assessment Tool (SWAT) hydrological model. We also quantified the uncertainties associated with GCM structure, greenhouse gas concentration pathways (RCP 2.6, 4.5 and 8.5), and prescribed increases of global temperature (1–6 °C) through streamflow changes. The SWAT model simulated historical monthly streamflow well, with a Nash–Sutcliffe efficiency coefficient of 0.66 for calibration and 0.62 for validation. Under RCPs 2.6, 4.5, and 8.5, the results indicate that annual precipitation changes of 1.01 to 8.88% and annual temperature of 0.60–3.21 °C will lead to a projected annual streamflow ranging from 0.91 to 12.95% compared to the historical period. The study indicates multiple climate change scenarios are important for a robust hydrological impact assessment.

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