The Museum's collection is one of the largest archeology collections in Israel. It is composed of various sub-collections, which all convey man's connection to the sea: underwater archeology; maritime art; maritime mythology; ancient anchors; Greco-Roman coins; scientific instruments (the Landau Family Collection); storage jars for maritime trade (the Collection in memory of David Kenneth); the Mediterranean Sea, its ports and islands - Phoenician ports and ports in the ancient land of Israel; cartography and prints (the Carl and Lee Handler Collection); shipping innovations; maritime battles; and maritime construction. A vast array of selected works from the collection is on permanent display at the Museum.
The Collection of Ancient Ship Models includes models whose construction was based on historical and literary sources, and on sculptural reliefs and murals preserved in palaces and tombs. These models present the evolution of warships and trading vessels in ancient Greece and Rome, the two maritime powers of the ancient world, alongside models of ships from the Byzantine period, the Middle Ages, the Age of Discovery, and the modern age.
The Numismatic Collection contains over a thousand coins decorated with maritime themes: ships, anchors, ports, pagan gods, fish, and seashells. In addition to the collection of Greco-Roman coins, the collection also includes a display of medals and medallions commemorating significant events in maritime history from the Renaissance to the present.
The Maritime Mythology Collection contains bronze and clay statuettes of pagan gods, the most striking of which are the statuettes of Aphrodite and Poseidon. The statuettes, together with the sea monsters and fish that adorn seals, clay candle holders, mosaics and maps, reflect a belief in the great powers of the sea.
The Collection of Scientific Instruments features navigational instruments from the 15th century onwards: astrolabes, compasses, telescopes, hourglasses and measuring instruments. Astronomical instruments made in China during the 1st century B.C.E. also appear in this collection.
The Collection of Storage Jars for Maritime Trade includes a vast array of clay artifacts that were drawn out of the water. These artifacts represent a cross-section of over three thousand years of maritime trade in the Mediterranean's Eastern Basin.
The Cartography and Prints Collection contains over 3,500 maps and engravings. This collection reflects the golden age of cartography in the Age of Discovery, when maps were made more accurate and color was first put to use. The collection also includes a unique group of maps of the Holy Land.
In 1997, the collection of the Museum for Ancient Art was added to the collection of the National Maritime Museum. Ancient artifacts that are not related to the sea are thus now exhibited alongside the displays concerned with maritime archeology.