Transport systems are capable of contributing to the economic robustness of a geographic area and the well-being of its inhabitants via the supply of the necessary assets for the mobility of people and goods. However, transport projects have the capacity to produce several negative externalities such as water pollution, air pollution, barrier effects, noise, and ecological impact, which affect the quality of people’s life. Considering these facts, the main purpose of this study is to indicate methodologically how the negative externalities of transport are interlinked, so that to promote sustainable mobility development. This paper reveals via the method of structural analysis, the interrelations between the negative externalities of transport, firstly to organize them hierarchically and secondly to evaluate the potential of sustainable mobility strategies concerning the co-benefits generated by their implementation for society. The results show that the negative externalities of transport are not isolated phenomena; on the contrary, they are interlinked and can be organised hierarchically according to the relationships between them so that certain public policies can be prioritized and the negative impacts of transport can be tackled more effectively. The most critical negative externalities are the invasion of public space for the construction of more roads, along with road accidents, congestion, and local air pollution. On the other hand, the most important group of strategies for sustainable mobility are the ones oriented to urban design, and more specifically to transit-oriented development.