About 132,000 years ago the course of the river changed southwards at Schaffhausen and formed a new channel, which also filled up with gravel. Part of the Rhine today includes this ancient riverbed.
During the Würm glaciation, the Rhine was pushed far to the south to its present course, over a hard Late Jurassic limestone bed. As the river flowed over both the hard limestone and the easily eroded gravel from previous glaciations, the current waterfall formed about 14,000 to 17,000 years ago. The Rheinfallfelsen, a large rock, is the remnant of the original limestone cliff flanking the former channel. The rock has eroded very little over the years because relatively little sediment comes down the Rhine from Lake Constance. http://flic.kr/p/BWz4et