That's a very common misconception, and the very one that destroyed my pool plaster by an incompetent acid washing crew, who only rinsed the acid off with water. Water
does not "stop the reaction" of acid. Only a neutralizing base does, like baking soda or ammonia mixed with water.
The build up you describe is typically removed with pressure blasting (using beads or other media). I'm not sure if that's because that's the best way to do it well, or if it's because the companies that offer this service don't want to take the chance of using acid on the tile to have it run down onto the plaster, or both.
I can tell you from my own experience that trying to remove pool water residue (presumably calcium and perhaps other compounds) from glass windows required manual abrasion. My Polaris pool cleaner's tail would regularly spray the windows, which was ignored for years by the previous home owner. My stone guru applied every type of chemical he had, including very strong acids, and the stains would not budge. We finally had to abrade it off using a very fine compound (with water, no acid) and a hand polisher. Which is what I recommend you try. I don't see you being able to control the acid well enough, its strength nor its whereabouts, to avoid damage to the pool (finish or mortar).
The product I used is called "Glass Renew" and this guy's address is on the label:
Dave the Grout Guy - San Jose Granite, Limestone, Marble Grout Repair. I don't know if he sells the stuff, I got my jar from my stone guy, who swears by this product. At the very least, maybe give Dave the Grout Guy a call and describe your situation. Maybe he'll sell you the same stuff, or maybe he'll have a better solution. If there was any abrasion done to the glass by the process and materials I used, I can't see it. My windows are crystal clear now.
To be thorough, I couldn't say what this stuff might do to the water chemistry. That'd be a question for Dave.
If you decide to try acid anyway (which I don't recommend), I suggest you do it in a very small area, the least visible, to see how, or even if, it'll work. And be sure you have some sort of neutralizer on hand, one that you've practiced with on some throw-away material, so that you can quickly neutralize the acid should something go wrong. The other mistake my acid washer performed: they blasted the entire pool with acid before they noticed it was destroying the plaster.
Strike all that. Don't use acid.
And it wouldn't be one of my posts, of course, if I didn't encourage you to wear the appropriate protective gear for whatever you're working with: for eyes, skin, lungs, etc.
Let us know how it goes, and what worked. I'm sure your solution could be used by others here.