There is a strong imbalance in EU transport mode shares. In addition, issues like road traffic, noise, accident rates, and especially polluting emissions result not only in external costs to society, but also in high logistical costs to transport service customers. The present paper proposes an assessment model to evaluate final internal and external costs of transport chains served by trucks and short sea shipping (SSS). An efficient and fast tool is presented to help customers decide on the most convenient mode of transportation for a specific trade link. The trade links in this paper connect 19 Spanish provinces to the main ports in the Black Sea region (Bulgaria, Georgia, Romania, Russia, Turkey, and Ukraine) through the ports of Barcelona and Valencia.