Traffic is one of the basic factors of effective and efficient development of economy of a country, and one of the subgroups of traffic is water traffic. In this paper, the emphasis is on sea transport, and maritime domain and seaports. Port, regardless of which classification is used, is the main object for any form of water transport – a dock for the ship. According to the purpose, ports are divided into ports open to public traffic and ports for special purposes. For a better understanding of the theory into practice, and to understand the system of sea ports, sea ports management system will be analyzed. One of the ports for special purposes is a nautical tourism port. In recent decades one of the most active branches of tourism is nautical tourism, as a separate branch of tourism, and the basic and most important object of this kind of tourism is the marina. Unlike some other countries, such as Italy, Croatia still needs to pay more attention to the development of the existing marinas and the construction of new ones. The management system of nautical port (marina) will be analyzed as an example of the management of port for special purposes.