My advice would be to get a clear plastic tub about four inches high and section off half of the tank with this, put the water fall in it. Fill it up with rocks so the pump intake in covered and so the toad can climb out easily. I've never had a toad drown on me in 3-4 inches of water, not even southern/texas toads. As long as you provide a way out they will find it.

I make this suggestion because Toads often like dry soil and will often advoid sopping wet sand/soil (which is what yours will probally be since the water runs under the entire tank).