The Black Well at Culloden is also called The Dead Well, and the well o wearie was connected with the legends of all those women that were killed there too, which got me thinking on connections between these two names, apart from the obvious fact of black being a mourning or negative colour.
The connection to death I thought of was that some wells were actually shafts, dug in celtic times with funerary or votive deposits in the bottom. T D Kendrick describes some which had a tree placed upside down in them, postulating a path climbing downwards to the underworld as well, perhaps for sacrificial messages to be carried, though that is speculation, obviously. Other well shafts have had little votive offerings, and animal bones in them, as well as those with human remains.
I'm wondering now if a black well might be something like the red water wells, like the chalice well mentioned earlier in the thread. Is there anything that might make the water black, apart from peat? Peat wouldn't be poisonous though, I guess. Just wild speculations of my own, but sometimes you get a breakthrough bouncing ideas around. A light bulb over the head moment...