The sea is home of a large variety of human activities creating social, economic and even strategic value for Europe’s inhabitants. Maritime activities have been concentrated around fishing, defence and shipping, although other human activities are increasingly taking place in marine areas. Some of those new activities have been growing substantially creating significant value for Europe’s maritime economy. Governments are aware of the need to better and more coherently management of seas in the European Union, being the Integrated Maritime Policy an umbrella for this approach. Maritime Spatial Planning is defined as a process of analyzing and allocating the spatial and temporal distribution of human activities in marine areas to achieve ecological, economic and social objectives. The Mediterranean Sea as a vast area covering twenty-two states from three continents, is an scenario where an increasing number of stakeholders have become aware of the urgency to find the right balance between economic benefits and (in their relation with the environment) the use of maritime space. The presented paper is going to apply the route planning in the short sea traffics linking peninsula with the Balearic Islands within a Maritime Spatial Planning scenario and evaluating their environmental performances. Some proposals will be suggested for a better coexistence between the maritime traffic and the protection of environmental sensitive areas.