John Calvin Commentary Joshua 4:9

"And Joshua set up twelve stones in the midst of the Jordan, in the place where the feet of the priests that bare the ark of the covenant stood: and they are there unto this day." — Joshua 4:9 (ASV)

And Joshua set up twelve stones, etc. Apparently, there was no use for stones under the water, and it might therefore seem absurd to bury stones at such a depth. The other stones, which were placed in Gilgal and were publicly visible, prompted inquiry; but stones hidden from people's eyes at the bottom of the water could have no effect in stirring their thoughts.

I admit that a monument entirely buried in silence would have been useless. But when they talked among themselves about the evidence of the passage left there, hearing about what they did not see strongly confirmed their faith. The ark of the covenant was kept in the sanctuary and covered by a veil placed before it; yet, its hidden splendor was still beneficial when they learned from the Law that the covenant of God was deposited in it.

It might also happen that, when the river was low, the tops of the pile would sometimes appear. But what I have already said is more probable: that even though Joshua buried the stones in the middle of the stream, he performed a useful act by establishing a testimony in the presence of the people, which would later become a topic of general conversation.