There are a few different methods that might remove water stains from unfinished wood, including attempting to buff the stain out with a light sandpaper or steel wool and using a warm, dry iron on a clean cloth and applied to the stain. Untreated wood that is regularly exposed to water should also be treated with a food-safe, shelf-stable product, such as castor oil, mineral oil or beeswax. One way to avoid water stains and other liquid stains is to use vinegar to clean the unfinished wood and rapidly wipe it up after it is sprayed on.
In addition to trying to spot clean untreated wood to remove water stains, light sanding the entire length and width of the wood's surface might help. This will help resmooth the surface and remove any stains and other marks that may have cropped up with use. Those people using power sanders should take care not to gouge any deep marks in the wood, instead aiming for a smooth, uniform surface. Starting off using a low-grit sandpaper and gradually moving up to a slightly higher grit (100 and then 200, for example) will help prevent the possibility of going too far with the sanding.