Prediction of rainfall-runoff process, peak discharges, and finally flood hydrograph is essential for flood risk management and river engineering projects. In most previous studies in this field, the precipitation rates have been entered into the models without considering seasonal and monthly distribution. In this study, the daily precipitation data of 144 climatology stations in Iran were used to evaluate the seasonal and monthly pattern of flood-causing precipitation. Then, by determining the rainy seasons and seasonal fit of precipitation with a probabilistic model and using regional precipitation, a semi-distributed conceptual model of rainfall-runoff (MORDOR-SD) was trained and validated using the observed discharge data. Flood prediction was performed using climatic data, modeling of hydrological conditions, and extreme flow data with high performance. According to the results, the Nash–Sutcliffe and Kling–Gupta coefficients were 0.69 and 0.82 for the mean daily streamflow, 0.98 and 0.98 for the seasonal streamflow, 0.98 and 0.94 for the maximum discharges, and 0.57 and 0.78 for low flows, respectively. Moreover, the maximum daily discharges in different return periods were estimated using the results of the MORDOR-SD model, considering the probability distribution function of the probabilistic model of central precipitation (MEWP), the probabilistic model of adjacent precipitation, and probability distribution function of the previous precipitation. Finally, the extreme flows were predicted and compared using different methods including the SCHADEX, regional flood analysis, GRADEX, and AGREGEE. The results showed that the methods GRADEX, AGREGEE, and SCHADEX have the highest performance in predicting extreme floods, respectively.