The permanent exhibition is structured in chronological order and includes four sections: ancient, medieval, modern and contemporary history.

In the first rooms three-dimensional objects - bas-reliefs, casts after epigraphic documents, coins, graphic works, convey information about the beginning of navigation on these in the space between the mountains, the Danube and the Sea. The generous space of over 10,000 square meters is organized into 22 thematic halls, which include numerous exhibits deeply related to the history of the city and the navy.

A special importance is given to the foundation of the three West-Pontic cities, Histria, Tomis and Callatis, to the interference of the material and spiritual culture of the Greek colonists with that of the Dobrogean natives. In the many years of coexistence between the native Geto-Dacians and the Greek world, complex relationships were established. Probably some of the numerous Getae from Dobrogea were employed as sailors in the crews of Histrian, Tomitian or Callatian ships.

With the help of models, graphic works, photographs and numerous original objects, the main exhibition of the museum illustrates the entry into service of new military and commercial ships, the training ship "MIRCEA" (II), presents the evolution of naval schools, issues related to of the establishment of the Romanian Naval League. Romania's entry into the Second World War, in 1941, reoriented the country's naval policy towards the execution of missions imposed by hostilities.