I was always under the impression that the well's initial state, where it seems like fresh water and gives you a boost, is the illusion and the deception - it seems nice when the landscape seems nice; this bugs out if you see through and dispel the landscape before confronting Ethel.
After you confront Ethel, the deception is dispelled and revealed - you've been chugging human remains and rotten tainted water all this time; she delights in your suffering, and you feel sick. After she is dead, the well is properly revealed to be the polluted stagnation that it really is and always was (at least as long as she's been lairing here), just like the rest of the swamp... however, none of this, not your awareness of its state or how it appears to your senses, ever changes the fact that it gives you a buff when you drink (it's hard to tell what's bug and what isn't, however)
