Small and medium-sized ports in the Baltic Sea Region find themselves in a dilemma to participate in the governance of innovation policies such as Smart Specialisation. The Smart Specialisation policy introduced by the European Commission supports regional economic and innovation development focusing on regional strength through selection of defined priorities, offering smaller ports an opportunity to overcome their dilemma. Currently, all European regions are monitoring and evaluating their performances alongside with the Smart Specialisation policy to make adjustments for the upcoming funding period. The Blue Growth concept entitles a large contribution to reach the emphasised goals and thus, ports can be an important actor and key driver for a sustainable and green future development. Hence, this paper analyses the current significance of smaller ports in Baltic Sea NUTS-2 regions reflected in the individual RIS3 maritime and/or logistic priorities as well as Blue Growth sub-sectors from the funding period 2014–2020 to contribute to the future design of RIS3. Yielded results will illustrate whether regional governances are aware of the potential small ports bring up to their economies with consideration to Smart Specialisation, Green Deal and Blue Growth Strategies and how RIS3 might effects small port performances.