- Model collection – a rich collection of ship models from the Middle Ages to today, as well as lighthouse models.
- Ethnographic collection – different tools and requisites, used for ship- and boat building, on sailing ships, in coastal fishing and the personal belongings of the coastal people and sailors in everyday-life and on travels. Parts and the equipment of the watercrafts, ship decorations and nameplates. Mast of the sailing ship “Triin” is the star exhibit of the collection.
- Maritime technical equipment collection – navigation and rescue equipment, ships’ wheels, propellers, and lighthouse equipment and much more
- Textile collection – uniforms and accoutrements of the Estonian Navy and commercial fleet are the most valuable part of this collection. Flags and banners are also preserved in the collection. The blue-black-and-white Estonian flag, dating from 1919, under which members of the navy marched on the 1st anniversary parade of the Republic of Estonia, is a real rarity.
- Badge collection – maritime-related medals and badges. More than 50 per cent of it is made up of former captain Lev Burak’s collection entitled Nautical History.
- Naval weapons collection – the largest collection of naval weapons in Estonia. The oldest among them – naval guns originating from the eighteenth century.
- Historical objects – items from the ships, of the mariners and the maritime organizations, personal belongings, souvenirs and gifts .
- Watercraft collection – different types of watercraft, most of which are included in the main exhibition at the Seaplane Harbour.
- Underwater archaeology collection – objects salvaged from sunken ships, enabling to date the ship and determine her origin. The most unique part of the collection is the shipwreck of the medieval cog with its findings. The collection grows by occasional finds because modern principles of research and protection of underwater heritage focus on study on the spot.
- Nautical charts collection – the oldest nautical charts in the collection date from the late eighteenth century. Among the rarest items is a hand-drawn map of the port of Tallinn from 1856. There are complete collections of nautical charts from the Estonian Republic and Soviet period.
- Documents collection – the oldest documents originate from the early nineteenth century. The collection is thematically classified as follows: Eesti Riiklik Merelaevandus (Estonian National Shipping Company), Veeteede Valitsus (Waterways Authority); ports, rescue stations, lighthouses; shipbuilding; sailing; fisheries; handwritten materials of sailors; maritime education.
- Art collection – this collection is made up mainly of oil or watercolour paintings and graphics. It also contains a collection of maritime-themed bookplates. The works stored in the collection depict different types of ships, ports, fishing, and the life of coastal people. The most valuable parts of the collection are the so-called captain’s paintings (i.e. paintings commissioned by captains to depict their ships in profile). The best known among them are works by R. Chapell and F. Tammik.
- Photo collection – photographs, postcards, and photographic negatives of maritime-related objects and persons. Cyanotype and ferrotype prints are also represented. One of them is coloured over and, as such, known as the only one surviving in Estonia. The oldest photo album in the collection dates from the late nineteenth century. The best-known photographers represented are C. O. Bulla and N. Apostol.
- Depot library – mainly study materials, handbooks, and atlases of the late nineteenth and the twentieth centuries that have belonged to sailors or nautical schools. A part of this collection was donated in a gathering campaign even before the Museum was established. The signatures of sailors and stamps of nautical schools and other institutions in a number of books can also be considered valuable.
