The agency will help an international consortium of shipping experts encourage more freight to be moved along Europe's network of rivers and sea routes instead of on the already congested roads and rail network.
The project, known as PROPS, will run for 36 months. Bell Pottinger will also be involved in running a series of marketing workshops across Europe.
This is the first time the EU has agreed to fund a professional comms agency's involvement in such a project. The account is believed to be worth six figures.
'With all the turbulence in the international economy at the moment, short sea shipping provides a cost-effective and more sustainable option than many other transport forms', said Bell Pottinger Business & Brand MD Kevin Read.
Bell Pottinger will analyse the existing ways short sea shipping is promoted to the maritime and freight industry, create new messages and provide EU member states with tools to promote the new messages.