Port authorities are modifying their nature and their role, acquiring more and more an active role in the governance of logistics systems and often adopting managerial and entrepreneurial behaviours. One common supporting tool of port authorities evolution and strategies could be identified into transportation flows modelization in order to assess the impact of policies in the modal distribution of the traffic flows (e.g. from road to sea) and the impacts that this shift may have in term of reduction of the emissions. The proposed methodology is based on the construction of a transport simulation model in order to check the modal distribution in different scenarios. The model can be used to compare the market dynamics (based on transport costs) with reference to different scenarios (number and frequencies of lines) and to the different costs involved. In such a way it is possible to compare and simulate the introduction of new lines on one side and the impact of Mos policies and projects on territories (in terms of regional impact in modal shift from road to MoS). The gravity model used in this work shows that the socio-economic and environment impact of Motorways of the Sea (MoS) depends more on environmental policies integration in the transport and logistics chain, territorial potential and importance of logistics systems rather than distance and transportation cost factors.