Environmental and social concerns force logistics firms to evaluate various risk factors for intermodal transportation systems. In this context, this paper takes into account economic, social, and ecological risk factors that have attracted considerable attention toward sustainable transportation. In this paper, the allocation of export containers to transportation modes, by incorporating social and ecological risks with a main focus on the minimization of transportation costs, was examined. A mixed-integer-programming-based mathematical model was proposed to decide how the containers can be allocated to different transportation modes. In addition, a fuzzy-based approach was performed to determine the social and ecological risk weights of the transportation modes within the decision process. Each mode was evaluated with social risks (e.g., human accidents and deaths) and ecological risks (e.g., emission values and noise pollution) by decision makers via the assignment of numerical scores. The obtained results show that optimal transportation modes more economical and environmentally friendly were provided by the proposed methods.