You make a good point about the water holes having no evidence of water marks... I like.
Agreed, they look more like joist gaps, but perhaps a little close together (vertically) also not in an even line (horizontally), or any indication of floor levels.... argh!? can't quite tell the dimensions in there tho, so not confident on a dismissal of this idea, anything but!
Looks like a dark dungeon, but also intrugued by the theory of a water way...
I keep wondering if there is something in the pic which would indicate its origin, but can't quite see it yet... hmm.
EDIT: drainage holes, yes, i think...