Getting Stuck In The Water Temple - Part 2

To conclusively determine if it's possible to get permanently stuck in the Water Temple, I've created an accurate mapping of the dungeon, to get a feel for the dungeon's natural flow.

The start of the dungeon is really interesting, because while the main room branches off into over 10 different pathways, only a handful of them can be fully explored.

Now I know the next bit is a bit much, but it should help you get a full mental picture of the layout of the dungeon

Of the rooms that are inaccessible at the start...

• All three rooms on the western side of the dungeon are inaccessible from the start. The 3rd and 2nd floor pathways are blocked by locked doors, while the 1st requires the water level to be lowered so that a platform that floats on top of the water makes a platform that allows Link to push the block away. The floating platform also serves as a means to prevent the player from opening the 2nd and 3rd floor doors without the water level being set at the proper level. 
• On the 3rd floor you have a door to the north which leads to the room containing the boss door. A floating hookshot target, which is out of the standard Hookshot's reach, prevents you from reaching the door without the water level at the 3rd floor. However, since there are no keys or switches in the room, it can be ignored.
• The 2nd floor (not shown above) has a room to south that is blocked by a timed gate which eventually leads to a block puzzle for a key. You can open it by shooting an eye switch below the entryway, but the gate shuts so fast that you can't simply swim past it. Rather, you are to stand on the platform in the middle of the room on the second floor, and use the Longshot to hit the hookshot target.
• On the 1st floor there is a pathway to the south that is blocked with a floor that can be broken up with a bomb, which don't work well underwater. Only a Golden Skulltula can be found that way, so the room can be ignored.
• Lastly, there are two doors which lead inside the center room. A locked door on the 1st floor is inaccessible as it requires another floating block platform to be settled on the ground. On the 2nd floor, there is a barred door which can be opened by lighting a nearby torch, but no magic in the game can start a fire underwater.

And for the accessible rooms...

• On the 3rd floor you have a room to the east which contains a simple block puzzle which rewards a key. To complete it, you are to enter the block puzzle room from the 3rd floor entrance and pull the block forward, then later on use the Longshot to get past the gate on the south side of the 2nd floor and push the block away to reach the key chest. 
• On the 2nd floor there is another room to the east which leads to the compass. Since the room has no locked doors to contend with, the room can be ignored completely.
• Lastly, on the 1st floor there is pathway a room that is three stories high, which again is on the east side of the main room. This room is where Nintendo intends to push you toward so to change the water level in the 3rd floor of this room. It's not shown, but at the top of this room there is also door that leads to a small room with the map in it, which can be ignored.

From this, there are two important things to point out. First of all, until you change the water level down to the 1st floor you cannot obtain a single key, and thus cannot ruin the dungeon right off the bat. Second, the only door accessible without changing the water level is the door to the Map Room. This prevents us from breaking sequence with Farore's Wind, since the way it works is that every time you pass through a door a mini-checkpoint is created, which is stored as a return point when Farore's Wind is cast.

With the water level changed, you can now access the two keys in the eastern and western rooms on the first floor, and unlock the center room.

More importantly, everything is set up for a potential bottleneck, since...

• The switch to lower the water level to the 1st is located on the 3rd floor
• Both keys can only be obtained while the water level is at the 1st floor
• Only one key is needed to raise the water level to the 3rd floor.

Which means that if we raise the water level to the second floor having only obtained one key, the second key cannot be obtained without cycling the water level back to the 1st floor. Fortunately, when we do raise the water level...

...we gain access to two more keys, and only one more locked door before we can freely cycle through all water levels, and obtain any of the four keys we missed. Similarly to the first two keys, these two keys (and actually, the key which requires the Longshot as well) can only be obtained while the water is at the 2nd floor.

Finishing everything up, once you obtain the first four keys, you should have two remaining to unlock the pathway to the mini-boss and the Longshot. From there, you only need two more keys: one at the end of the Snake River (which comes immediately after obtaining the Longshot), the other from completing the block pushing puzzle. These final two keys will let you obtain the Boss Key, and finish the dungeon.

To recap:

• The locked doors can be paired into three groups: 
• Two stop you from cycling through the water levels
• Two more stop you from reaching the Longshot, and require the water to be at the 3rd floor
• The final two stop you from collecting the Boss Key, and requires the Longshot
• No keys can be obtained with the water level at the 3rd floor, and the path to the Longshot cannot be unlocked without the water level at the 3rd floor.
• The two keys on the first floor and the two on the second give you more than enough to unlock the first two doors, and allow you to freely cycle the water level, obtain four keys, get the Longshot and finish off the dungeon

So Nintendo's design is properly thought out. It should be impossible for the average player to get permanently stuck in the Water Temple by using a key in the wrong order.

You would think that would be all there is to say, but you're wrong. In the next part, I intend to look into ways on how to make the dungeon permanently unbeatable.