Two of the halls are dedicated to the marine achievements of the prehistoric and ancient times. The presentation is mainly performed through ship models.
The first sea trip in the world for which there is documented evidence took place in the Aegean and concerned the transportation of obsidian from Milos to the Cave of Frangthi in Argolis 10,000 years ago. This has been a great attainment of early navigation, since the primitive stone tools available at the time did not allow the construction of complex vessels. The Corfiot papyrella, the primitive vessel which was still being constructed until the 20th century by few craftsmen at the village of Liapades in Corfu, is a probable descendant of the Mesolithic vessels that performed those first sea trips. Clear evidence of the strides in shipbuilding and the existence of the strong naval supremacy of the Minoans and their successors, the Mycenaeans, is the representation of ships belonging to the 2nd millenary BC on signets, engravings and primarily on the murals with the so-called “Fleet” at the West House of the murals in Santorini, dating back to 1550 BC approximately. A reference to this stage of evolution is made by the models of the Minoan vessel and the so-called “Ship of Thera”. Around the middle of the 13th century BC and a little later, the civilizations of eastern Mediterranean were shocked by massive invasions of new populations which swept away the peoples already inhabiting the area and signaled the beginning of the “dark centuries” period which was to last approximately until the 9th century. During that period, however, significant rearrangements took place in the Aegean which provided the appropriate conditions for the ensuing rise of the Greek civilization of the archaic and classical age.

There are numerous ship representations dating back to the end of that period. A characteristic vessel of those days is the pentekonter, a type of war ship already used in the Homeric years. Taking a close look at the model, the visitor identifies the basic characteristics of those archaic war ships: slender and long, with many oars and the typical ram on the bow.The apex of the development of war vessels is the Athenian trireme of the 5th century BC. The fast oar-powered vessel with the mighty ram brought many victories to the Athenians and its greatest moment was the sea battle of Salamina in 480 BC which crowned the Athenian supremacy in the seas spreading from the straits of Messina of Sicily to the coast of Asia Minor. Centrally in the hall, there are two large models (versions) of the trireme which is the masterpiece of ancient Greek shipbuilding.
Those floating war machines are surrounded by models of their moorage facilities, the well known “neosoikos” (ship shed) and the Arsenal of Philon, namely the ammunition warehouse of the Ancient Athenian fleet. The merchant marine activity of the archaic and classical age is represented by two extremely elaborate models of concave merchant vessels, whose construction was based on the findings of the shipwreck which was discovered in Kyreinia of Cyprus and dates back to 303 BC. Building details and vessel parts have been represented on these models, while special emphasis has been placed on the way commodities were stored in their hold. These models are accompanied by a small collection of pointed-base amphorae, storage urns which were the usual cargo of ancient merchant boats. A clear allusion for the visitor of the historicity of the Museum premises is the incorporation in its exhibition area of the architectural relics of the 4th ce. BC Cononian fortification built to protect the coast of Piraeus. Archeological findings from the nearby area have been placed at the same spot. The most important of them are the six pyramidical stone anchors which were hauled up from the bottom of the small harbour of Zea and date back to the 5th to 4th ce. BC.