The application of two distinctively different hydrologic models, (conceptual-HBV) and (distributed-BTOPMC), was compared to simulate the future runoff across three unregulated catchments of the Australian Hydrologic Reference Stations (HRSs) namely Harvey catchment in WA, Beardy and Goulburn catchments in NSW. These catchments have experienced significant runoff reduction during the last decades due to climate change and human activities. The Budyko-elasticity method was employed to assign the influences of human activities and climate change on runoff variations. After estimating the contribution of climate change in runoff reduction from the past runoff regime, the downscaled future climate signals from a multi-model ensemble of eight GCMs of the CMIP5 under the RCP 4.5 and RCP 8.5 scenarios were used to simulate the future daily runoff at the three HRSs for the mid-(2046–2065) and late-(2080–2099) 21st-century. Results show that the conceptual model performs better than the distributed model in capturing the observed streamflow across the three contributing catchments. The performance of the models was relatively compatible in the overall direction of future streamflow change, regardless of the magnitude, and incompatible regarding the change in the direction of high and low flows for both future climate scenarios. Both models predicted a decline in wet and dry season's streamflow across the three catchments.