Is there a way to get black water spots out of raw oak flooring?
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Sand off any finish, and use wood bleach on the spots, keep reapplying till it lightens up to shade desired, then use a damp rag to remove any excess. Dry throughly, then use a spray top coat to blend in the finish, be sure to get the same finish of satin or semi-gloss.
http://www.howtocleanstuff.net/how-to-remove-stains-from-unfinished-wood/
Here's another way to get rid of the black marks and keep them off.
https://www.hunker.com/12433566/how-to-get-black-spots-out-of-wooden-floors
Best of luck on your project!