Boatswain Bay () is an uninhabited waterway in the Qikiqtaaluk Region of Nunavut, Canada. It extends eastward from James Bay into the headland, a part of Quebec.
Characterized by salt marshes, brackish marshes, open sea, and inlet habitats, the bay stretches , with an elevation ranging up to above sea level.
Due to the number of migratory birds the Boatswain Bay Migratory Bird Sanctuary was established in 1941. As a bird sanctuary it is a Canadian Important Bird Area (#NU097), a Biodiversity Reserve, and a Key Migratory Bird Terrestrial Habitat site.