I have a similar setup; the sub is about 7" deep.

My frog is an adult though.
There shouldn't be a problem as long as you replace the substrate regularly and mix up the soil every so often.
You should also avoid making the substrate overly wet, which along with sub replacement and mixing, will help alleviate problems with pooling and stagnant water.
That all said, you should probably keep it in something smaller until it grows into the tank. As it stands now, it looks like he can't even get into or out of the water without jumping high (if he can manage it at all).