There is a strong imbalance in EU transport mode share. In addition issues like road congestion, noise, accident rate and especially pollutant emissions result not only in external costs to society but also in high logistical costs to customers of transport services. The present paper proposes an assessment model to evaluate final internal and external costs of transport chains served by road and short sea transport as an efficient, fast tool to help customers decide on the most convenient transportation mode for a specific trade link. The links in this work connect Spanish Mediterranean coasts and the Black Sea with up to 19 Spanish provinces, with freight being imported and exported from/to Barcelona and Valencia and the main ports of Bulgaria, Georgia, Romania, Russia, Turkey and Ukraine.