The answer to 'skylight water stains' is that they are typically caused by leaks around the skylight. Common symptoms include water stains, discoloration, or mold growth on the ceiling or walls around the skylight. Solutions can range from simple DIY repairs to more complex professional roof work, depending on the severity of the issue.
If the stains are minor and localized, you may be able to fix them yourself by inspecting the skylight, sealing any cracks or gaps, and applying a waterproof sealant. However, if the leaks are more extensive or the damage is significant, it's best to call in a professional roofing contractor to properly diagnose and repair the problem.