Untreated wood surfaces turn up black marks when water puddles on them over a period of time. Oxalic acid will get those black marks out. Barkeeper’s Friend is the thing to use as it has oxalic acid. Make a milky paste of Barkeeper’s Friend and water and set it on the marks. Let it sit for at least five hours. When you come back to it the marks should be gone. In some cases it may need a second application.
Note: The acid may whiten the wood. This is definitely not a strategy for fine woods. And on any wood, be sure to wipe up the paste on any areas outside the region of the black mark.