Wipe the surface of the counter with a damp rag to see if you can remove the stain simply by washing the surface.
Sand the surface of the countertop with 80-grit sandpaper, a medium grit for scrubbing off surface imperfections. You can use a block wrapped in sandpaper or an electric sander. Always work with the grain of the wood or the sandpaper will cut obvious scratches in the surface of your countertop.
Wipe away the wood dust from the surface of the countertop with a damp rag to check periodically if the stain is still there. Continue sanding until no trace of the water remains.
Wipe the surface of the countertop again, working with the grain and rinsing the rag often. Wring out the rag well to remove the excess water.
Seal the countertop surface with an inert oil that won't become rancid over time. Examples of suitable oils include white mineral oil, raw tung oil, raw walnut oil or raw almond oil. With the exception of the tung oil, these oils never dry on the surface of the wood but are soaked into the wood, keeping it water-repellent, not resistant. Tung oil does dry to a somewhat shiny finish after several coats. Spread an even coat of oil over the wood with a dry rag and allow it to stand overnight. Wipe off the excess in the morning with a clean rag.
Apply new oil every week, or after heavy scrubbing, to keep the wood in good condition and maintain its ability to resist water stains.