Sorry for resurrecting an old post.. but if anyone else finds this using the search function I would like to add my two cents. While in college I worked at a Marina for a number of years and as low man on the totem pole I was responsible for acid washes and other terrible jobs like cleaning the bathroom when people unexpectedly went on the floor (and not the puddle kind..) Unfortunately acid washing pontoons is quite tricky and requires more care than fiberglass hulls. Our policy was to tape off any metal near the toons that we didn't want to get damaged, and then wet down the anodized fencing and other areas far away but susceptible to overspray. We would do the toons in small sections to minimize the amount of time acid sits to prevent etching but still trying to maintain a uniform finished appearance (pretty tricky). Despite my best efforts a couple boats a year would get unexpected damage. One pontoon, I can't remember the brand, ended up with severely etched toons. We didn't really do anything different than normal so was odd but the acid reacted poorly or the material was slightly different. I had to sand and polish to mirror finish to correct. There were a couple times where overspray got on the anodized fences or one time even the fumes discolored a stainless rub rail. Like others have said, no way to fix those and get perfect matched coloration, stains were permanent. Need to re-anodize or replace. For mild cleaning, there are other products that are still harsh but not as bad as muratic acid. For a carpet of algae, I only found muratic acid to work.
Also acid washing sucks. Terribly. Full protective suit, goggles, and respirator while carefully spraying muratic acid but trying to work quickly, often when its still hot out or sometimes even worse when its near freezing cold for minimum wage is awful. My suggestion: get a boat lift! No need for acid then. A used pontoon lift can be found for a few grand. We used to charge at least $500 for an acid wash and that was years ago.