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The unbalanced evolution of the environmental normative in the European Union for the different transport modes has led to a broader debate about whether Short Sea Shipping is still a green transport mode. This discussion is especially pertinent because there is no technological alternative indisputably identified as the most adequate one to meet the emission requirements in the emission control area without penalizing the competitiveness of Short Sea Shipping. The objective of this article is to assess the performance of intermodal chains versus trucking in terms of costs, times, and externalities when the selected fleet for Short Sea Shipping is made up of optimal container vessels operating with different propulsion plants and fuels in compliance with emission control area requirements. This is, Tier III-four-stroke diesel engine with marine gas oil, a Tier III-four-stroke diesel engine Tier III with scrubber and heavy fuel oil, and a four-stroke dual engine operating with liquefied natural gas. To this aim, a mathematical model, which is able to provide optimized technical and operative features of the vessels, is modified and solved for an intermodal chain between Spain and France through the Atlantic coast. This study shows that dual liquefied natural gas engines prove to be not only the most sustainable solution but also the most suitable in terms of costs, as long as the difference in price between liquefied natural gas and petroleum fuels is equal to the base case or within a modification range of 20%. This study also highlights that due to the limited range of Short Sea Shipping vessels, the loss of the cargo capacity in holds by the gas tanks arrangement was not significant.