Incomplete hydro-meteorological data and insufficient rainfall gauges have caused difficulties in establishing a reliable flood forecasting system. This study attempted to adopt the remotely sensed hydro-meteorological data as an alternative to the incomplete observed rainfall data in the poorly gauged Kuantan River Basin (KRB), the main city at the east coast of Peninsula Malaysia. Performance of Weather Research and Forecasting (WRF) schemes’ combinations, including eight microphysics (MP) and six cumulus, were evaluated to determine the most suitable combination of WRF MPCU in simulating rainfall over KRB. All the obtained results were validated against observed moderate to extreme rainfall events. Among all, the combination scheme Stony Brook University and Betts–Miller–Janjic (SBUBMJ) was found to be the most suitable to capture both spatial and temporal rainfall, with average percentage error of about ±17.5% to ±25.2% for heavy and moderate rainfall. However, the estimated PE ranges of −58.1% to 68.2% resulted in uncertainty while simulating extreme rainfall events, requiring more simulation tests for the schemes’ combinations using different boundary layer conditions and domain configurations. Findings also indicate that for the region where hydro-meteorological data are limited, WRF, as an alternative approach, can be used to achieve more sustainable water resource management and reliable hydrological forecasting.