Typhoons and storms have often brought heavy rainfalls and induced floods that have frequently caused severe damage and loss of life in Taiwan. Our ability to predict sewer discharge and forecast floods in advance during storm seasons plays an important role in flood warning and flood hazard mitigation. In this paper, we develop an integrated model (TFMBPN) for forecasting sewer discharge that combines two traditional models: a transfer function model and a back propagation neural network. We evaluated the integrated model and the two traditional models by applying them to a sewer system of Taipei metropolis during three past typhoon events (NARI, SINLAKU, and NAKR). The performances of the models were evaluated by using predictions of a total of 6 h of sewer flow stages, and six different evaluation indices of the predictions. Finally, an overall performance index was determined to assess the overall performance of each model. Based on these evaluation indices, our analysis shows that TFMBNP yields accurate results that surpass the two traditional models. Thus, TFMBNP appears to be a promising tool for flood forecasting for the Taipei metropolis sewer system.