From the perspective of risk transmission process of basin water resources security, this paper systematically analyzes fundamental concepts, including the water resources security system, water resources security risk system, and water resources security risk assessment. The conceptual framework for water resources security risk assessment is proposed, which is characterized by an Aristotelian syllogistic relational structure and encompasses five elements: the hazard of risk-inducing factors, the vulnerability of risk-bearing bodies, the risk-inducing potential of hazardous environment, the risk-resistance capacity of mitigation measures, and the water resources security loss risk. This paper reveals the transmission mechanism of water resources security risk elements, where under specific risk-incubating and risk-resisting conditions in a watershed, the hazard of risk-inducing factors serves as the system input, the vulnerability of risk-bearing bodies as the system transition, and the water resources security loss risk as the system output. This paper elaborates on methodology for water resources security risk assessment, consisting of water resources security risk assessment objects, evaluation indicators, evaluation indicator measurement methods, methods for quantifying qualitative indicators, single-indicator evaluation methods, methods for determining indicator weights, and methods for determining comprehensive evaluation indicators. The theoretical framework composed of the conceptual system, risk transmission mechanism, and risk assessment methodology forms a preliminary theoretical foundation for water resources security risk assessment. This theoretical framework also holds significant application value for risk assessment in other resources and environmental systems.