Inland and short sea ships and their ports is a critical part of Europe’s transport system. With stricter requirements on decarbonization and reduced noise and pollution from the transport sector, the importance should only increase! However, the convenience and flexibility of road transport still tend to trumph the sustainability goals. The AEGIS project has been selected by the EU Commission to show that autonomous ships and automation in ports can make waterborne transport much more flexible and user oriented, while continuing to reduce the societal and environmental impact of EU transport. This will be the “Advanced, Efficient and Green Intermodal Systems” - AEGIS. Small ships and inland barges can decongest roads, reduce noise and dust pollution, while operating on batteries or other non-carbon fuels. By automating ports and terminals and use these to integrate larger long distance ship operations with new and smaller ship types, a completely new European transport system can be developed. More flexible and user centric transport, better services to rural as well as urban areas and a revitalization of the regional ports and city terminals is the goal.