I don't mean to hijack this thread, but I have the exact same problem. My rock is flagstone, I don't know if that is any more porus or softer then sandstone, but anyway here is what I have done so far. I have tried the pumice stone trick, forget it, I got to one piece of rock and half the pumice stone was gone and the calcium was still there. I tried using a wire brush, no difference, then on the outside of the pool I tried CLR, I hate to say it but I've never been impressed with that product and I'm still not, it didn't even make a dent.
Okay, to move on, I tried a brass wire brush hooked up to my drill motor (this was in the spa, and I had drained all the water out) while this made a small difference it was very time consuming and I still could not get all the calcium deposits off, that stuff is extremely hard, it also did not hurt or discolor the stone, but I do want to try and polish out some of the areas I worked on. Next I tried a mixture of muratic acid, a small wire brush, elbow grease and a very small screwdriver. This worked better then anything else I tried, but still very very time consuming. I only have about an eighth of the spa done.
The small screwdriver was for chipping off the calcium, I felt like a dentist!! But I didn't hurt the stone, the mixture of MA and water seemed to work but frequent rinsing due to me worrying about hurting the grout. Other than that I just bought a product from Home Depot which is specifically made for cleaning hard water stains. It is a very strong concentration of Hydrochloric Acid. I have not tried this yet, since I tried the MA first and it did not work that well. I also tried the vinegar trick, that was no help. I did not know Harbor Frieght had a glass bead setup, that might just be my next item to try. So there you have it from my personal experience, if all else fails I will just go back to the MA, wire brush and screwdriver. If I come up with anything that does work I will be sure to post it here!