Data-driven models using an artificial neural network (ANN), deep learning (DL) and numerical models are applied in flood analysis of the urban watershed, which has a complex drainage system. In particular, data-driven models using neural networks can quickly present the results and be used for flood forecasting. However, not a lot of data with actual flood history and heavy rainfalls are available, it is difficult to conduct a preliminary analysis of flood in urban areas. In this study, a deep neural network (DNN) was used to predict the total accumulative overflow, and because of the insufficiency of observed rainfall data, 6 h of rainfall were surveyed nationwide in Korea. Statistical characteristics of each rainfall event were used as input data for the DNN. The target value of the DNN was the total accumulative overflow calculated from Storm Water Management Model (SWMM) simulations, and the methodology of data augmentation was applied to increase the input data. The SWMM is one-dimensional model for rainfall-runoff analysis. The data augmentation allowed enrichment of the training data for DNN. The data augmentation was applied ten times for each input combination, and the practicality of the data augmentation was determined by predicting the total accumulative overflow over the testing data and the observed rainfall. The prediction result of DNN was compared with the simulated result obtained using the SWMM model, and it was confirmed that the predictive performance was improved on applying data augmentation.