Into the mighty waters, i.e. the deep waters, such as these were, into which, when a stone is thrown, there is no hopes of seeing it again.
Related Commentaries of Nehemiah 9:11
Nehemiah 9:11
11 And thou didst divide the sea before them, so that they went through the midst of the sea on the dry land; and their persecutors thou threwest into the deeps, as a stone into the mighty waters.