Flowing water has time and the almost boundless energy of a planetary weather system. In the Flats, most of the deposition takes place where the current is slowed by vegetation and shallow water. The erosion is concentrated in and near the channels. These effects are modified by changes in the overall level of the Great Lakes system. When the water is low, these effects are exaggerated.
Shallower water means less water flowing directly out of the main channels through the marshes.
The water must go somewhere, so it rushes through the smaller channels, scouring them out. The slow water in the marshes has time to drop more of its load of sand and silt. The water, with other places to escape, is flowing slowly in the little cuts and channels, allowing sand and silt to be deposited which gradually fills in the channels, which in turn sends more water through the marshes. The sharp drops in level that leave parts of the marshes nearly dry and scour out the little channels haven't occurred for a long time. Check out the Army Corp of Engineers Historic Hydrographic Data .