At the bottom of a disused siege well in some partly water filled caverns a monster has recently become active due to a rock fall bringing it water. It’s dispersing spores, influencing villagers in their sleep.

So what else will the party encounter down there? I’m looking for critters that could plausibly have survived all this time without revealing their presence by, for example, emerging to eat people and livestock.

Well (LOL), there are several creatures worldwide in folklore and myth which traditionally live in wells; and then there's the group of relatively long-lived amphibious D&D monsters which don't necessarily need meat to survive (not 'obligate carnivores', as the technicalispeak goes.)   OR they ,might do their hunting elsewhere; as a longtime DM since the early days of D*D the first question that immediately pops into my mind is, "Does this well connect to the Underdark, or to a passage or crevice (collapsed or not) that does?"  You have a lot more options if so, but even if it doesn't there's still the two subsets of monsters I mentioned above.  Off the top of my head. again;

FOLKLORE WELL-DWELLERS                                                                                         OTHER D&D MONSTERS THAT might WORK

Ach ssss, <gollum>?                                                                                                          Aboleth

  (couldn't resist this one, a family friend corrupted me with The Hobbit at the age of ten, and by my eleventh birthday I'd pestered my parents into getting me a box set of LOTR for my present)

Kappa (Japanese)                                                                                                              Black pudding (could eat other creatures in the well, and would not                                                                                                                                            necessarily be noticed if it did come out bc. of camouflage)

Vodyanoy (Russian creature; sometimes charmed its victims                                                                                                                                                                   rather than eating them and making them disappear)

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EDIT: Sorry, just read the full text about this monster dispersing spores that affect victims in their sleep.  That definitely sounds like a creature on the mind flayer spectrum, such as an aboleth.  In fact, I think one of the published adventures explores a similar situation, of a hidden creature using some form of mind control  (as well as shapeshifting/illusion?) to lure unsuspecting villagers to their doom.  I also don't know what level adventurers you're designing this for; aboleth's a pretty bloody powerful creature.  But there are lesser DC monsters in the same toolkit (creatures from the fallen  mind flayer Underdark empire) that would also work

(WIP)

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