It occurred to me that particular aetheryte might be surrounded by water deliberately, as the aetheryte's hamlet is in the middle of a secure underground research facility containing lifeforms from all over Hydaelyn in a simulated environment whose climate and ecosystem is very carefuly controlled - the water around the aetheryte was therefore probably for decontamination purposes (cleaning dirt that might have contaminants or outside diseases on the soles of your feet from outside Labyrinthos) - presumedly arriving in the lift has you undergo something similar where your boots are cleaned before leaving the lift, but we don't see it.

Either way, that's just my take on it.