Motorways of the Sea present a practical example of combined and sustainable transport. With respect to the present model of functionality of the transport system in the Republic of Croatia, where the development of the port and of the gravitational transport system is left to each individual port (six independent ports), and where there is no systematic approach to specialization of each port or route, the results of the analysis are not promising. The goal of this research is to explain why the current Motorways of the Sea implementation model is inefficient and unsustainable. The analysis shows that a scientific approach to multicriteria analysis, which includes the identification of all relevant factors, the analysis of the transport infrastructure, as well as the identification of criteria which could potentially affect the Motorways of the Sea system, can correctly define the optimal model for the implementation of a sustainable Motorways of the Sea system.