The methods to assess water pollution risk for medium water transfer are gradually being explored. The event-nature-proportion method was developed to evaluate the probability of the single event. Fault tree analysis on the basis of calculation on single event was employed to evaluate the extent of whole water pollution risk for the channel water body. The result indicates, that the risk of pollutants from towns and villages along the line of water transfer project to the channel water body is at high level with the probability of 0.373, which will increase pollution to the channel water body at the rate of 64.53 mg/L COD, 4.57 mg/L NH4(+) -N and 0.066 mg/L volatilization hydroxybenzene, respectively. The measurement of fault probability on the basis of proportion method is proved to be useful in assessing water pollution risk under much uncertainty.