Those are the remains of the timber sets that supported the walls & roof (horizontal timbers have fallen/floated off). I suspect that as the level is driven in boulder clay or similar & fills to the roof with water, all the small, fine stuff in the walls & roof has crumbled & 'dissolved', possibly flowing out to day when in flood, leaving only the big rocks. I've seen this in a number of places in the Pennines & Lake District - you end up with a very big level!
The water is just a puddle - if you don't want to be first through it, I will.
Cheers
Heb