The MFU's governance is determined by an annual convention of the General Assembly and is represented by its Maritime Council and its provincial Councils. The MFU Executive is headed by the President, two Provincial Vice Presidents and a Secretary-Treasurer.

The most important structure of the organization is based on a wharf representation system. Its more formal framework uses a network of locals, divided as follows

Nova Scotia
Local 9 : Southwest Nova Scotia
Local 6 : Eastern Cape Breton
Local 4 : Southern Northumberland Strait

New Brunswick
Local 10 : Baie des Chaleurs
Local 1 : Acadian Peninsula
Local 3 : Northern Northumberland Strait
Local 2 : Central Northumberland Strait
Local 5 : Southern Northumberland Strait