First of all, if the water stains are in the finish they can be solved with Wood Elixir. Also, if the finish is still on the desk, then Wood Elixir will remove the stain you applied and put it back to the original color. I think you realize now that you can't hide water marks with wood stain. Stains are formulated to be absorbed into the wood. If there is a finish on the wood, the stain will sit on the surface and will not bond with the finish. This fact allows Wood Elixir to remove the wood stain and repair this finish.