The purpose of the article is to analyze the technical implementation tools of integrated development of rail and sea transport systems in multimodal transportation in their modern conception. The authors of this article analyzed studies and practical approaches in the field of multimodal transportation with the participation of rail and other modes of transport. The authors suggested improving the organization of the movement of material flows in a multimodal transport system by developing models for organizing multimodal transportation based on the theory of inventory management, probabilities, and mass service. The article presents the results of the analysis and theoretical generalization of approaches to the formalization of the operation process of the dynamic multimodal transport systems with the participation of rail and sea transport.