This paper introduces a decision support tool for sustainable intermodal chains with seaborne transport, in which the optimization of a multi-objective model enables conflicting objectives to be handled simultaneously. Through the assessment of ‘door-to-door’ transport in terms of costs, time, and environmental impact, the most suitable maritime route and the optimized fleet are jointly calculated to maximize the opportunities for success of intermodal chains versus trucking. The resolution of the model through NSGA-II algorithms permits to obtain Pareto fronts that offer groups of optimized solutions. This is not only useful to make decisions in the short term, but also to establish long-term strategies through assessment of the frontiers’ behavior obtained when a sensitivity analysis is undertaken. Thus, consequences of transport policies on intermodal performance can be analyzed. A real-life case is studied to test the usefulness of the model. From the application case, not only the most suitable Motorway of the Seas with their optimized fleets are identified for Chile, but also significant general findings are provided for both policy makers and heads of ports to promote the intermodal option regardless of their geographical locations.