It can usually be cleaned with an acid. Vinegar should work. An acid toilet bowl cleaner such as The Works from Walmart should work better. It contains hydrogen chloride (ie hydrochloric acid). Keep it away from metals and rinse thoroughly. - pauleckler
I have tried all sorts of things for that waterline discoloration in the toilet bowel. Various bowel cleaners, chlorine bleach, oxy clean powder paste, comet paste (but no scrubbing, CLR, all with minimal effect, the faint line was still visible.
Finally as a last resort, I reached for the hydrochloric (muratic) acid, the high strength stuff used to adjust PH in swimming pools. Multiple applications, No effect. If straight HCl won’t work, I don’t see how a wimpy vinegar product would stand a chance. Just sayin’