Transport, especially road transport as one of the modes and a dominant one, has a negative impact on the environment and the society. This is manifested through frequent transport congestions, increased risk of accidents, increased noise levels, increased stress for all stakeholders and the society in general, large amounts of exhaust gas from vehicles that is emitted directly into the environment and fumes discharged in the process of motor fuel production. Motorways of the Sea are maritime services integrated in the door-to-door logistic chain by using sustainable, regular, frequent, high-quality and reliable short sea shipping connections. Motorways of the Sea are a practical example of the definition for a combined (sustainable) transport. It is intermodal transport mode where maritime transport covers the largest part of the route. Motorways of the Sea system does not require significant infrastructure investments in ports, but success of the service presupposes excellent integration with other transport modes, notably rail and road. The fact that interaction with various transport modes takes place in a port, makes the port a significant factor in the formation of a competitive Motorways of the Sea system. Equally important is the communication and the flow of interaction with a ship, railway or road system because if only one link is not impeccable, it will be reflected in the reliability and quality of the entire system and service. In relation to the current model of the transport system functioning in the Republic of Croatia where development of port and gravity transport system is left for each port independently (six individual ports), and where systematic specialization of each port and route does not exist, the results of an analysis are devastating. The results testify that current model of the Motorways of the Sea implementation is entirely inappropriate and there is no element that would justify its retention. Analysis implies that scientific approach which includes identification of all relevant factors, state of the art analysis of entire transport infrastructure and identification of criteria which affect the functioning of the Motorways of the Sea system, can safely and accurately determine which model is optimal for the introduction of sustainable Motorways of the Sea system and can determine the evaluation of the current model. From the impact analysis of each individual criteria and all the combinations, it may be concluded that two scenarios (models) may be recognized as optimal choices for the implementation of a sustainable system on the example of the transport system of the Republic of Croatia. These two models are: a model of two ports and a model three ports.