Identification of reliable alternative climate input data for hydrological modelling is important to manage water resources and reduce water-related hazards in ungauged or poorly gauged basins. This study aims to evaluate the capability of the National Centers for Environmental Prediction Climate Forecast System Reanalysis (NCEP-CFSR) and China Meteorological Assimilation Driving Dataset for the Soil and Water Assessment Tool (SWAT) model (CMADS) for simulating streamflow in the Muda River Basin (MRB), Malaysia. The capability was evaluated in two perspectives: (1) the climate aspect—validation of precipitation, maximum and minimum temperatures from 2008 to 2014; and (2) the hydrology aspect—comparison of the accuracy of SWAT modelling by the gauge station, NCEP-CFSR and CMADS products. The results show that CMADS had a better performance than NCEP-CFSR in the climate aspect, especially for the temperature data and daily precipitation detection capability. For the hydrological aspect, the gauge station had a “very good” performance in a monthly streamflow simulation, followed by CMADS and NCEP-CFSR. In detail, CMADS showed an acceptable performance in SWAT modelling, but some improvements such as bias correction and further SWAT calibration are needed. In contrast, NCEP-CFRS had an unacceptable performance in validation as it dramatically overestimated the low flows of MRB and contains time lag in peak flows estimation.