Explaining the significant variability of rainfall in orographically complex mountainous regions remains a challenging task even for modern raingauge networks. To address this issue, a real-time spatial rainfall field estimation model, called WREPN (WRF Rainfall-Elevation Parameterized Nowcasting) model, has been developed, incorporating the influence of mountain effect based on ground raingauge networks. In this study, we examined the effect of mountainous rainfall estimates on the uncertainty of flood model parameter estimation. As a comparison, an inverse distance weighting technique was applied to ground raingauge data to estimate the spatial rainfall field. To convert the spatial rainfall fields into flood volumes, we employed the ModClark model, a conceptual rainfall–runoff model with distributed rainfall input. Bayesian theory was applied for parameter estimation to incorporate uncertainty analysis. The ModClark model demonstrated good flood reproducibility regardless of the estimation method for spatial rainfall fields. Parameter estimation results indicated that the WREPN spatial rainfall field, which accounted for the influence of the mountain effect, led to lower curve numbers due to higher estimated rainfall compared to the IDW spatial rainfall field, while the concentration time and storage coefficient showed minimal differences.