The introduction of autonomous systems in maritime transport is fundamentally changing the approach to shipping, providing increased safety, reduced operating costs, and increased efficiency. At the same time, these innovations pose a number of challenges, especially in the areas of decision-making and risk management. This chapter explores the integration of advanced models, such as decision trees and Bayesian networks, with robust risk management strategies to effectively deal with the uncertainties and threats that accompany the deployment of autonomous vessels. Real-life cases of implementing these models in practice are analyzed, emphasizing the importance of adaptive strategies and real-time decision support systems to ensure reliable and safe operation of autonomous vessels, contributing to the long-term sustainability of maritime operations.