Sequential advances and retreats of the Laurentian ice sheet repeatedly opened and dammed various possible outlets from the area, as well as providing dramatically varying amounts of meltwater to the system.

[9][10] Ongoing warping of the land by post-glacial rebound due to the retreat of the glacial ice continued to modify the drainage structure of the region, allowing the reunification of all three basins (Superior, Michigan, and Huron) as the Nipissing Great Lakes.

The current configuration of the lakes reflects the latest step in a long history of their post-glacial evolution.

Although the Straits create a pronounced bottleneck in the contours of the shoreline and a major constriction in the local bathymetry, defining two distinct basins, they are still deep and wide enough to allow the free exchange of water between the two sides.

[14][3] The combined effects of seiches (some being resonant standing waves)[15] and of differing weather conditions (atmospheric pressure, wind)[14] over each basin act to drive water either way through the Straits on a variety of characteristic timescales, at amounts sometimes exceeding 75,000 m3/s (2,600,000 cu ft/s) for several hours in either direction.

[3][4][22] Because of the hydrologic connectivity through the Straits, some sources consider the total area and volume of Lake Michigan–Huron when placing this system in a global or regional context.