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Safety, progress, and investment risks are correlated during the construction period of large-scale water transfer projects. However, previous studies have only considered individual risk factors, overlooking the potential systemic risk posed to safety, progress, and investment, as well as any underlying common cause failures. Since traditional risk analysis methods are ill-suited to addressing common cause failure, this paper's objective was to establish a comprehensive evaluation index framework and to identify the basic events of common cause failure. To do that, we developed a risk analysis method that models common cause failure based on a Bayesian network for assessing that systemic risk. The Henan Section of the Yangtze-to-Huaihe River Water Diversion Project in China was then used as a case study. The results show that a variety of common cause failure events, such as epidemic disease, design alteration, lagged approval process, heavy rain in the flood season, renewal material and failing equipment, construction accidents, and external interference, can significantly impact the safety, progress, and investment systemic risk. Design alteration poses the greatest risk, with renewal material and failing equipment exerting the strongest influence among all common cause failure events. It is also possible to elucidate the predominant causal chains; specifically, the contributing influence of each basic failure event to the systemic risk can be clarified by adjusting their respective initial state. The failure of renewal material and failing equipment was found to significantly increase the safety risk. This study effectively simulated the complex causal relationships and uncertainties of pertinent risk factors, thereby enhancing our understanding of the systemic risk associated with safety, progress, and investment in large-scale water transfer projects. [ABSTRACT FROM AUTHOR]