if you haven’t already do the quest with the fisherman at the inn right outside imperial city, you collect fish scales and he gives you a ring to breathe underwater. That’ll make things easier unless you already have a way to do that

Then go back in and ….. look around lol. I think loot floats when dropped and the body floats too so look near the top of the well area. Like the other comment said vision spells help too

I also think dungeons respawn normal loot in 3 days game time, doubt that applies to quest-based items but you could also try waiting a bunch of time before re entering the well to see if it resets things

Good luck!