The purpose of this paper is to examine the existing warning stages of the target stations in the Tan-shui River basin and to propose suitable warning and emergency stages. First, historical damages during the flood periods and the hydrographs of water surface elevation of the target stations are analyzed. Necessary actions that the government and people should take are also discussed. Referring to the strategy adopted by other countries, such as Japan, America, and Mainland China, the definitions of the warning and emergency stages for Tan-shui River are proposed. Seventeen representative sets of historical typhoon floods are selected. On the basis of the inundation area and depth data, we analyze the rising speed of the floods, and the critical inundation elevations of the river banks or levees. Second, some circumstances should be considered including: (1) limited sample size of the historical typhoon floods, and (2) the uncertainties of the hydrological conditions, including the rainfall in the watershed and the sea level during typhoon period. Thus besides 17 sets of historical flood events, 187 synthetic sets of flood events are generated. Third, the rising speeds of the stages for the total 204 sets of food events at target stations are computed by using 1-D numerical channel-network hydraulic model. According to above approaches, the warning and emergency stages of the target stations in Tan-shui River can be determined more practically and precisely because the hydrological uncertainties of the watershed are considered.