Perhaps most obvious option is bottle duplication. Considering the many different ways that bottle duping can be done, it's entirely conceivable that someone may accidentally overwrite the hookshot/longshot slot with a bottle, crippling movement throughout the dungeon. However, Bottle Adventure makes it possible to "equip" a hookshot/longshot on B. Furthermore, it's possible to always recover certain "ammo" items even after being bottle duped over by collecting or buying them, meaning that BA is always a potential option. Since I'm not particularly familiar with the nuances, and not particularly interested in looking into this angle further, I can't say for sure if you can get permanently stuck doing this.
So instead, I'd like to look back to the Water Temple itself. To refresh, the intended design of the dungeon looks like this:
- Two locked doors prevent cycling water between F1-F3 freely (F1 Center, F2 West)
- Two locked doors (F3 West Path) block access to Dark Link/Longshot. These doors can only be opened when water is at F3
- Two locked doors (F1 North Path) prevent access to the Boss Key. No keys are along this path
- Two keys only obtainable with water level at F1
- Two keys only obtainable with water level at F2
- Two keys only obtainable with water level after obtaining Longshot ("Snake River" Key, F2 South -> F3 East key behind block)
- No keys can be obtained at the dungeon start
And now the so called "solution":
To become "permanently stuck", the solution is to lock at least one of the F1 keys underwater, without unlocking the ability to cycle through the water levels freely. To do this, you can obtain one of the following keys without changing the current water level:
- The F2 key behind the bombable wall, along the F1 east path which leads to the F1 water level switch. This is done by using a Bombchu to destroy the cracked wall, as they don't diffuse instantly when touching water. The chest itself can be opened underwater by hooking onto it with the Hookshot. This resets a "grounded" state, allowing it to be opened.
- The F2 South -> F3 East key behind the large block. This is done by utilizing a glitch that allows you to roll while the block is moving
With a key in hand, backtrack to the main room, and enter the F3 West path. Cast Farore's Wind.
If you collected the F2 key behind the bombable wall, backtrack to the F1 water switch and lower it to F1. Now you have three options:
- Obtain one of the two F1 keys, and use that to unlock the center room to raise the water level to F2
- Savewarp, jump to the second floor platform and enter the center room with an Arrow and raise the water level to F2, locking both F1 keys underwater.
- Obtain the F2 South -> F3 East key behind the large block, and use it to unlock the door leading to the center room to raise the water to F2, locking out both F1 keys.
If you collected the F2 South -> F3 East key behind the large block, make sure to collect the F2 key behind the bombable wall, and use it to unlock the center room.
Either way, the only key obtainable now should be in the center room under the floating block. Collect it, and restore the Farore's Wind point. Use it to unlock the second door leading to Dark Link's room, and backtrack to the main room.
It should now be "impossible" to make progress, due to the following facts:
- The water level is at F2, but the F2 West door leading to the F3 water switch is locked.
- 1 or 2 keys are stuck on F1 which can't be accessed
- 1 or 2 keys require the Longshot
Sadly, this solution is fairly flimsy since it's very easy to reach the F3 water switch regardless of the current water level.