The demand for freight transportation services is a derived demand and is strongly influenced by the spatial organization and management of supply chains. In recent years, numerous trends affecting the spatial organization and structure of supply chain-logistical systems have emerged. These trends have developed as a consequence of the rapidly changing political, economic, social, and technological environments. The rational planning and design of the freight transportation system should consider these emerging trends in order to respond efficiently to the requirements imposed by the new organization of logistical systems. The objective here is twofold: first, to propose a methodological framework for developing and assessing scenarios describing the evolution of the freight transportation system characteristics due to the emerging logistical trends and, second, to apply the proposed framework to assess the future development patterns of the freight transportation system for a number of industrial sectors in Europe. The results of the proposed methodology led to identifying the relevant importance of the various logistical trends influencing the organization, utilization, and performance of the freight transportation system. The research results provide an insight into the development of the freight transportation system for different types of movement (i.e., primary, secondary, and so forth) and transportation modes. The proposed methodology provides decision makers with a tool for developing and simulating alternative policies regarding the future development of the freight transportation system.