Efficient planning of freight transportation requires a comprehensive look at wide range of factors in the operation and management of any transportation mode to achieve safe, fast, and environmentally suitable movement of goods. In this regard, a combination of transportation modes offers flexible and environmentally friendly alternatives to transport high volumes of goods over long distances. In order to reflect the advantages of each transportation mode, it is the challenge to develop models and algorithms in Transport Management System software packages. This paper discusses the principles of green logistics required in designing such models and algorithms which truly represent multiple modes and their characteristics. Thus, this research provides a unique practical contribution to green logistics literature by advancing our understanding of the multi-objective planning in intermodal freight transportation. Analysis based on a case study from hinterland intermodal transportation in Europe is therefore intended to make contributions to the literature about the potential benefits from combining economic and environmental criteria in transportation planning. An insight derived from the experiments conducted shows that there is no need to greatly compromise on transportation costs in order to achieve a significant reduction in carbon-related emissions.