The article is devoted to the study of the principles and regularities governing the formation of cause-and-effect relationships in the system of safe ship operation. It is determined that numerous factors, including the technical condition of the vessel, crew competence, navigation conditions, cargo characteristics, port infrastructure, and environmental requirements, influence the safety of navigation. The authors propose a comprehensive assessment methodology that involves identifying key factors, determining their weighting coefficients and probabilities of occurrence, and calculating integral safety indicators at each stage of the operational process. Particular attention is paid to the role of the human factor and the interaction of socio-technical components in ensuring safety. The developed model enables consideration of the interrelationships between technical, navigational, technological, and environmental safety components, allowing for the prediction of the overall level of flight safety. The results can be used to enhance safety protocols, improve the efficiency of risk management, and inform decisions in the maritime industry.