If the water stain is on the base side of the film, I have had success using a very soft lens cleaning tissue to wipe it off. I place the negative emulsion side down on a tissue on a flat tabletop and using another dry tissue, firmly wipe the area where the water mark is present. This usually removes the stain although a few passes may be required.
Note that I only do this when the mark is on the base side of the film, not on the emulsion side which is much softer and prone to scratching. I also only use this technique with water marks. If the water mark is on the emulsion side, I rewash, Photo-Flo, and squeegee the film to remove the mark. Oily marks such as fingerprints need to be removed with a film cleaner.
If you are concerned that the procedure will scratch your film, try it on a frame you know will never be printed. Anytime the film surface is touched may lead to damage, but I've had 100% success with this method as long as the stain was on the base side of the film.