The primary inflows are Greenwater Creek at the southwest; the Kashabowie River at the north; and the Swamp River at the northeast.

The primary outflow is the Shebandowan River, which leaves Lower Shebandowan Lake over a weir at the east at the community of Shebandowan, and flows via the Matawin River and the Kaministiquia River to Lake Superior.

Ontario Highway 586 branches from Highway 11 along an isthmus between Middle Shebandowan Lake and Lower Shebandowan Lake.

The Canadian National Railway Kashabowie Subdivision main line, built originally as the Canadian Northern Railway transcontinental main line, also follows the north shore of the lakes.

Clockwise from the Matawin River outflow Other map sources: