So, I visited the sewers beneath Bream Island, randomly first, and on a quest (retrieving the doctor's book from the lady) the second time around. I found a lever there that activates something in a "well", but I wasn't able to find that well there, or on Bream Island, or really anywhere else I've looked.
Another issue I've had with that area is that I can't seem to open the final door with any key, nor can I unlock it. It must be connected to some quest or specific item/switch, but I haven't been able to find it. Help?