The intellectualization of water transport is accompanied by an expansion of the landscape of threats to transport security, caused by the characteristics and weaknesses of the technologies being introduced, which are the convergence of information and telecommunication technologies, automated and automatic control technologies and artificial intelligence. The peculiarity of these technologies is working with large volumes of information. Violation of the security of information processed in intelligent systems of water transport (illegal access, modification, deletion and similar unauthorized influence) causes a violation of transport security and, as a consequence, the security of critical information infrastructure and the country’s critical infrastructure, national security. Convergent technologies used in intelligent transport systems are characterized by multiple and poorly formalized manifestations of the consequences of threats. The article presents a model for assessing the risks of information security of intelligent water transport systems, based on the methods of the theory of fuzzy sets and fuzzy logic, the use of which makes it possible to take into account the above-mentioned features of the technologies being implemented. The hierarchical structure of the model and the use of fuzzy set theory and fuzzy logic methods make it possible to adapt the model to various risk criteria, types of input data and the level of detail of risk analysis. For the presented model, a methodology for assessing information security risks has been developed and an example of risk calculation is given. The developed model and methodology are intended to build an information security risk management system for autonomous shipping, implementing technologies of hybrid (augmented, extended) intelligence, providing for the use of artificial intelligence controlled by people.