Water Stains on Mahogany Beams

We are having a sunroom added onto our home. The sunroom has mahogany beams which I am polyurethaning outside. To protect them, from possible rainshowers, we covered them with a tarp for overnight. The tarp must have had some water on the underside and a couple of the beams now show some waterspots. I was hoping that they would disappear, however drying overnight, the spots still show as much as they did yesterday.
Should water stain mahogany like this?
Should the waterspot disappear when dry?
I've tried sanding, but the spot must a lot deeper than I want to sand. How can I get the waterspot out?
Larry Bohen
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