I have used CLR and like to see it foam when it is working. However, it is a bit expensive for cleaning rocks. I have had similar results with vinegar and time (what CLR will do in 20 min will take overnight with vinegar). Iron Out is a pretty good alternative too. Some people swear by coke cola, but I have not had much success with it. I also use some of the stronger acids (outside and with care).
One thing about CLR, that I learned the hard way, is keep the drips away from your countertop. It can pull the color right out, if it is not wiped up fairly quickly. I left some drops overnight which resulted in dime sized round white marks. The kitchen counters have since been replaced, so I am no longer in the doghouse. ;-)