5. Morpha
A giant amoeba possessing the water. You're in a pool-like room with some nice water, it wouldn't hurt to jump in, but NO you CAN'T jump into this pool because it's the boss!
It's very fitting to battle what is practically water in a watertemple. Water temple, boss, water. Makes complete sense. But then it doesn't make sense because how can you battle water?
That's what make this boss so genius. It also has multiple ways of being defeated, being cheap with the long shot, using din's fire, doing it how you're supposed to, whatever. It's water, it's easy to manipulate.
The strategy to defeat this boss has been repeated in many games after it, so strategy-wise it hasn't aged too great, but at the time this was a wonderful idea. For me, I always looked forward to the water temple just because of this boss battle.
It also makes sense why Lake Hyrule had been drained to a small pool when the boss is this guy. Sometimes the bosses don't really make sense as to why they're the boss or why they did whatever they did, but this guy makes completely sense.
