Well first of all, it was stated in OoT that the Deku Tree, Jabu Jabu and the Goron mines were all visited by Ganondorf which means that those places were infected by him so the monsters are there under his order.
Also, the water medallion doesn't reside in the water temple. The sage of water gives you the water medallion which is a physical manifestation of part of her power. The medallions aren't items in a chest that people can just randomly find.
Sorry, I worded that incorrectly. What I meant was they protected the access to the place that had the sages (I haven't played OoT in 4 years, so i can't remember what the name of this place was).
The overall point I was trying to make is that the ones in the temples aren't always evil, they may have been there to protect the gate into the sage room, or whatever treasure happened to be in that particular Temple/dungeon.
Bosses were obviously controlled by Ganon/dorf, because all of the bosses could not be normally encountered later. These bosses were ganon/dorf's way of protecting the gate to the sage room from Link, or any other hero for that matter, so that he could personally go in there eventually.
We don't ever know if ganon/dorf is really in his castle, or if he was just preparing to get the Medallions (or sage room, etc.) for himself.
Anyway, my major, core point to all of this is that not all of the enemies have to be evil. when some play a game, andhey see something attacking them, they automatically think "Ooh! An enemy who is evil", when it could really just put there by the Gods to protect access to the sage room sorrycalling it the "sage room". As I mentioned before, I don't know what the place is called).
Or they could just be an animal who wandered into the Temple. There could be several theories. But I'm sticking with mine.