In the coastal waters of Taiwan, freshwater discharge from rivers can be an important source of uncertainty in regional ocean simulations. This effect becomes especially acute during extreme storm events, such as typhoons. In particular, record-breaking discharge caused by Typhoon Morakot (August 6-10, 2009) was observed to significantly affect near-shore temperature and salinity during the Intensive Observation Period-09 (IOP09) of the Quantifying, Predicting and Exploiting Uncertainty (QPE) research initiative. In this report, a river discharge model is developed to account for the sudden large influx of freshwater during and after the typhoon. The discharge model is then evaluated by comparison with the discharge time series for the Zhuoshu and Gaoping Rivers and by its utilization as forcing in ocean simulations. The parameters of the discharge and river forcing models and their effects on ocean simulations are discussed. The reanalysis ocean simulations with river forcing are shown to capture several of the independently observed features in the evolution of the coastal salinity field as well as the magnitude of the freshening of the ocean caused by runoff from Typhoon Morakot.