As the custodian of the national maritime collection of Quebec, the Museum possesses more than 15, 000 artefacts, photos and old documents related to all kinds of maritime events.Some of the most precious collections include:
- Collection of objects having belonged to Captain Joseph-Elzéar Bernier and original photographs of many of his journeys
- Artefacts from the Empress of Ireland
- Collection of small traditional watercraft
- Scale models of ships
- Navigation instruments
- Lighthouse lenses and navigation aids
- Furnishings from ships
- Instruments to work underwater
The Museum is also the custodian of the sailing ship J.E. Bernier II and has two ship museums that can be visited from engine room to wheelhouse (hydrofoil Bras d’Or 400 and the icebreaker Ernest Lapointe).
The collection also includes the Fonds d’archives maritimes Armand Therrien (maritime legacy documents) entrusted to the Museum by Archives nationales du Québec between 1982 and 1995 (emphyteutic loan) and consisting of various files on maritime life in Quebec.