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

In the first rooms, three-dimensional objects - bas-reliefs, molds based on epigraphic documents, coins, graphic works, transmit information about the beginning of navigation on them in the space between the mountains, the Danube and the Sea. The generous space of over 10.000 square meters is organized in 22 themed rooms, which include numerous exhibits with a deep connection to the history of the city and the navy.

Particular importance is attached to the founding of the three western Pontic fortresses, Histria, Tomis and Callatis, to the interference of the material and spiritual culture of Greek colonists with that of the Dobrogea natives. In the many years of co-existence between the Geto-Dacian natives and the Greek world, complex relationships have been established. Probably some of the many Getae in Dobrogea hired sailors in the crews of the Histrian, Tomato or Callatian ships.

With the help of models, graphic works, photographs and many original objects, the basic exhibition of the museum illustrates the entry into service of new military and commercial ships, the school ship "MIRCEA" (II), presents the evolution of naval schools, related aspects 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 the unfolding of hostilities.