Rashi: They were uprooted from the water to the dry land by them, and the water returned to its place. It turns out that the Aron was on one side, and Yisrael on the other side, and the Aron carried its carriers. Uza was punished for this, when he grabbed the Aron (he thought that it is about to fall

Radak, Malbim: Had it all returned at once, it would have flooded greatly over its banks. Rather, the lower water (i.e. at ground level) descended with a little of the upper water (what had piled up), until it returned to normal, to be full until its banks.

Malbim: Charavah refers to what still has some moisture, or initially had water and it departed. There was no miracle on the banks; it remained moist. The Kohanim's feet went from the Yabashah (the middle of the river, which dried totally) to the Charavah (bank).