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The main characteristic of the water resources system (WRS) is its great complexity and uncertainty, which makes it highly desirable to carry out a risk analysis of the WRS. The natural environmental, social economic conditions as well as limitations of human cognitive ability are possible sources of the uncertainties that need to be taken into account in the risk analysis process. In this paper the inherent stochastic uncertainty and cognitive subjective uncertainty of the WRS are discussed first, from both objective and subjective perspectives. Then the quantitative characterization methods of risk analysis are introduced, including three criteria (reliability, resiliency and vulnerability) and five basic optimization models (the expected risk value model, conditional value at risk model, chance-constrained risk model, minimizing probability of risk events model, and the multi-objective optimization model). Finally, this paper focuses on the various methods of risk analysis under uncertainty, which are summarized as random, fuzzy and mixed methods. A more comprehensive risk analysis methodology for the WRS is proposed based on the comparison of the advantages, disadvantages and applicable conditions of these three methods. This paper provides a decision support of risk analysis for researchers, policy makers and stakeholders of the WRS.