The South—to—North Water Transfer (SNWT) Project is one of the four largest trans—boundary projects in China. With the construction and operation of the project, increased attention has been paid to the risk factors which are induced by the uncertainties. The analysis and management of integrated risk are also put before the project managers. It is extremely important to reduce and control the integrated risks involved in the operation of the project. In this study, Baoying Station on the eastern route of the SNWT Project was chosen as the study area, and Bayesian Network (BN) theory is used to evaluate the probability of the integrated risks. Based on the reasoning of BN, the final integrated risk probability of Baoying Station is estimated to be 0.025% and the risk level is “lower level”. Analysis of the scenario shows that the probability of integrated risk is most severe when management and maintenance conditions of the pump in use deteriorates. More attention should be paid to this important risk factor during the operation of the project.