You can clean water marks off of clear glass with CLR® Calcium, Lime & Rust Remover.
The question, though, from Rebecca in Spring Grove, Illinois was “Can CLR Calcium, Lime & Rust Remover be used for colored stained glass that has water marks on it from the sprinkler?” Rebecca, if the glass has been colored in the processing of the glass and not painted or coated after manufacture, CLR is safe to use on the glass only. If you avoid any contact with the lead or frame of the stained glass, CLR is safe to use as a diluted solution of equal parts CLR and warm water. Apply the solution using a damp cloth or sponge to the glass only. After 2 minutes, hand remove the solution from the glass using a damp cloth or sponge and clear cold water. Do not spray the glass directly to ensure that the CLR solution does not come into contact with the other materials in the stained glass piece.