I find Keil and Delitzsch's explanation reasonable:
But it cannot be so absolutely affirmed that these stones would be carried away at once by the stream, so that they could never be seen any more. As the priests did not stand in the middle or deepest part of the river, but just in the bed of the river, and close to its eastern bank, and it was upon this spot that the stones were set up, and as we neither know their size nor the firmness with which they stood, we cannot pronounce any positive opinion as to the possibility of their remaining. It is not likely that they remained there for centuries; but they were intended rather as a memorial for the existing generation and their children, than for a later age, which would be perpetually reminded of the miraculous help of God by the monument erected in Gilgal.