The quality of precipitation forecasting is critical for more accurate hydrological forecasts, especially flood forecasting. The use of numerical weather prediction (NWP) models has attracted much attention due to their impact on increasing the flood lead time. It is vital to post-process raw precipitation forecasts because of their significant bias when they feed hydrological models. In this research, ensemble precipitation forecasts (EPFs) of three NWP models (National Centers for Environmental Prediction (NCEP), United Kingdom Meteorological Office (UKMO) (Exeter, UK), and Korea Meteorological Administration (KMA) (SEOUL, REPUBLIC OF KOREA)) were investigated for six historical storms leading to heavy floods in the Dez basin, Iran. To post-process EPFs, the raw output of every single NWP model was corrected using regression models. Then, two proposed models, the Group Method of Data Handling (GMDH) deep learning model and the Weighted Average–Weighted Least Square Regression (WA-WLSR) model, were employed to construct a multi-model ensemble (MME) system. The ensemble reservoir inflow was simulated using the HBV hydrological model under the two modeling approaches involving deterministic forecasts (simulation using observed precipitation data as input) and ensemble forecasts (simulation using post-processed EPFs as input). The results demonstrated that both GMDH and WA-WLSR models had a positive impact on improving the forecast skill of the NWP models, but more accurate results were obtained by the WA-WLSR model. Ensemble forecasts outperformed coupled atmospheric–hydrological modeling in comparison with deterministic forecasts to simulate inflow hydrographs. Our proposed approach lends itself to quantifying uncertainty of ensemble forecasts in hydrometeorological the models, making it possible to have more reliable strategies for extreme-weather event management.