In the recent years, when the typhoon occurs, the degree of turbidity of water is increased and the consequence is the shortage of clean water. In order to mitigate this problem effectively, a research study had been performed to determine the necessity and feasibility of developing some back-up systems, like development of small reservoir and pipe network. But since, the existing water resources facilities would not hamper the environmental and sustainable development, this suitable water allocation policy would be better than that of developing a back-up system. Because a good water allocation policy can utilize the water resources in the most efficient manner. It may avoid developing back-up system which would not only require a huge amount of money but also low probability of usage in the future. Kaohsiung district's water supply system was used as a case study during Haitang (in 2005) and Billis-Kami (in 2006) typhoons. The Generalized Water Allocation Simulation Model (GWASIM) was adopted to evaluate the best water allocation process and compared its result with the site records. The analyzed result showed that when the Kaoping weir can't withdraw enough water, the shortage can be satisfied by other water resource facilities in this system or by the neighborhood Tainan district's water supply system. During the high turbid period, the water treatment plant ought to treat less water to avoid damaging the equipment and to decrease the treatment loading. In this way, the district could satisfy close to the demand and it would avoid severe shortage without using the back-up system. So, a suitable water allocation policy would be another economic and feasible option to solve the shortage problem effectively during high turbid period.