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To alleviate harm to the environment, short sea shipping (SSS) is gaining popularity in transportation policy formulation as an alternative transport mode for ecofriendly and cost-efficient transportation. There have been no studies of how to optimize intermodal container movement incorporating environmental aspects into SSS networks. This paper analyzes an intermodal transportation problem of international container cargoes while incorporating the external costs of the modes into an optimization model in South Korea. The objective of the problem is to minimize the total logistic costs, that is, shipping and land transportation costs, as well as external costs such as air pollutants (particulate matter, nitrogen oxide, sulfur dioxide, and volatile organic compounds) and greenhouse gases (carbon dioxide). The results of the model show a strong foundation for encouraging more environmentally friendly modes, such as SSS and rail, and a well-balanced modal shift if transport policy is formulated in this direction.