The shallow waters of the James Bay region represent an important late autumn staging area for migratory, Arctic-breeding waterbirds.

[2] Two migratory bird sanctuaries are located in the complex: the 14.6 square kilometres (5.6 sq mi) Moose River Bird Sanctuary is at the mouth of the Moose River, and the larger 238.3 square kilometres (92.0 sq mi) Hannah Bay Bird Sanctuary on the eastern coast of Hannah Bay at the mouth of the Harricana River.

[3] As many as 75,000 geese of various species may simultaneously use the staging area in autumn, and large populations of ducks are also easily observed.

Southern James Bay lies within the flat sedimentary basin of the Hudson Bay lowland in the Hudson Plains ecozone, and its coast is "characterised by a sequence of mudflats, intertidal marshes and supertidal meadow-marshes, which grade through a willow-alder shrub area into a drier forest interspersed with fens and bogs".

[3] Gradually rising inland from sea level, it attains elevations of no more than 50 metres (160 ft).