The Adriatic Sea is a unique and highly sensitive ecosystem. The economic development and social existence of its coastal states depend heavily on a clean and preserved Adriatic Sea. However, the Adriatic Sea is also a seaway used mainly by international shipping transporting goods to and from Europe (as hinterland), with intense local shipping as well. Of increasing concern is the introduction of harmful aquatic organisms and pathogens (HAOP) via ships’ ballast waters (BW). The general BALMAS objective is to establish a common cross-border system, which will link all researchers, experts and responsible national authorities from Adriatic countries in order to avoid unwanted risks to the environment from the transfer of HAOP. This will be achieved through control and management of ships’ ballast waters and sediments. Further, long-term effective ballast water management (BWM) in the Adriatic will be set at the cross-border level utilizing this project’s related knowledge and technology.