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The Water Temple becomes manageable when you treat its central chamber as a hub and the water level as a route selector. Set the level at one of the three Triforce marks, return to the hub, and re-check passages that are now underwater, exposed, or reachable from a different height. The middle-water setting is especially important: sink through the opening beneath the floating central platform to find a small key.
Before you start: identify your edition
This walkthrough covers both the Nintendo 64 original and Ocarina of Time 3D for Nintendo 3DS. The dungeon layout and overall progression are the same, but a few actions differ. On Nintendo 64, changing the water level means pausing to equip or remove the Iron Boots; on 3DS, the boots can be switched much faster. Producer Eiji Aonuma described the remake’s change this way: “Link can put on and take off his Iron Boots in a flash!”
The 3DS version also adds visual markings around some doors to make routes to water-level controls easier to recognize. Its camera presentation makes the opening beneath the rising central platform more obvious. In one crystal-switch room, walkthroughs place the switch behind the gate on Nintendo 64 but in front of it on 3DS, so do not apply a single platform-neutral instruction to that puzzle.
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| Nintendo 64 | Iron Boots must be equipped or removed through the pause menu; one crystal switch may be behind a gate. | The three Triforce controls, key progression, Dark Link, Longshot, Boss Key and Morpha route. |
| Nintendo 3DS | Iron Boots switch quickly; markings help identify water-control routes; the same crystal-switch room may place the switch in front of the gate. | The hub-and-water-level structure and major item sequence. |
If you are choosing a version rather than following a cartridge you already own, Ocarina of Time 3D is the Nintendo 3DS edition associated with these usability changes. Check the platform, region, condition and current listing separately when buying; availability and listings can change, and a guide or game listing should not be treated as a guaranteed price or permanent stock promise.
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What to have ready
The temple’s progression assumes that you can sink and float, activate distant targets and change the water level. Keep the Iron Boots and Hookshot readily available from the beginning. Zelda’s Lullaby is required at every Triforce mark. Bombs are needed for the cracked wall in the room where Ruto was found. Arrows or Din’s Fire can solve the torch puzzle at low water; arrows are useful because they let you carry a flame across a gap without walking into danger.
There is no single combat trick that replaces the route logic. If a door remains locked, first check your key count and water setting. If a target looks unreachable, remember that the ordinary Hookshot has a shorter reach than the Longshot you earn after Dark Link. Those checks prevent you from spending time trying to force a room that is deliberately waiting for a later item or level.
The route model that prevents you getting lost
There are three water settings: lowest, middle and highest. Each is activated by playing Zelda’s Lullaby at a Triforce mark. The controls are not one-use switches: you return to them whenever a later route requires a different level.
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- Lowest water: exposes lower floors and passages, including the opening sequence for several early keys.
- Middle water: raises the central platform and reveals the hole beneath it. This is where the often-missed small key is found.
- Highest water: opens the upper routes that lead through the Dark Link encounter and onward to the Longshot.
After every water change, go back to the central chamber before exploring elsewhere. Ask three questions: Which doorway was underwater before? Which ledge is now too high or too low? Did a platform, block or water spout change position? This hub reset is more reliable than trying to remember a linear route through rooms that change with the water.
Use a simple route ledger
To avoid repeating rooms, keep a short note with three headings: lowest, middle and highest. Under each heading, write the doors or rooms you have cleared and any chest you have opened. When you return to the hub, compare the current water level with that note. A room that was cleared at low water may still need to be revisited at middle or high water, while a room that has no new ledge or target can be left alone.
Keys are the best progress check. You should have the low-water torch-room key, the key from the drained hub’s spinning-water route, the key beneath the middle-water platform, and the key revealed by bombing the cracked wall near Ruto. Additional keys and the Boss Key come later. If a locked door stops you, count what you have already collected before wandering into every side room again.
Enter the temple, find Princess Ruto and collect the map
- At the entrance, remove the Iron Boots so Link rises to the ledge.
- Put the Iron Boots back on to descend through the water.
- Follow the route between the unlit torches until you find Princess Ruto.
- Follow Ruto upward, then enter the nearby room and open the map chest.
The Iron Boots control whether Link sinks or floats. The Hookshot is used for enemies and targets, so keep it ready while you move through the opening rooms. If you miss the ledge or drift past a target, change your boot state deliberately rather than swimming in circles.
Meeting Ruto is also a useful orientation point. The nearby map room gives you a reference for later returns, and the cracked wall in this area becomes important once the water is lowered again. Do not assume that collecting the map means the room is finished forever.
Set the water to its lowest level
Use the first Triforce mark
Return to the room containing the Triforce symbol and play Zelda’s Lullaby. The water drains to its lowest setting. This is the first time the temple’s route logic becomes visible: a floor that was submerged is now a usable path.
Open the torch door and take the key
- Drop through the opening in the central floor.
- Find the lit torch and use its flame to light the two unlit torches. You can shoot an arrow through the flame or use Din’s Fire.
- When the door opens, deal with or pass the Shell Blades.
- Open the chest for the small key.
If the door does not open, check that both unlit torches were lit. The flame must reach each torch; lighting only one does not complete the puzzle. This is a good place to practice the low-water route, because the same central opening becomes a landmark when you later raise the level.
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Explore the drained hub and the spinning-water route
Open the lower passage
Return to the central chamber. Move the large block into its hole to open a lower passage. Enter with the Iron Boots equipped so you can sink, then remove them at the appropriate point to rise through the next passage.
Cross the water-spout gap
Continue across the water-spout gap and enter the room with swirling water. Land on the underwater ledge rather than fighting the current from the middle of the pool. Your goal is controlled movement: sink to the ledge, establish your position, then use the target rather than letting the current choose your route.
Use the dragon-mouth switch
- Use the Hookshot to hit the switch in the dragon’s mouth.
- Use the wall target to cross the timed gate while it is open.
- Float upward after passing the gate.
- Collect the additional small key from the chest.
The gate is timed, so line up your target before activating the switch. If you arrive too late, activate the switch again instead of attempting a risky swim through the closing gate. The extra second spent setting up a clean shot is safer than being pushed back into the current.
Raise the water to middle and get the hidden key
Reach the second Triforce mark
Use the locked door at the base of the central tower. It leads to the second Triforce mark. Play Zelda’s Lullaby to raise the water to its middle level.
Find the opening under the floating platform
Watch the central platform rise. The movement exposes a hole directly beneath it. This is the answer to both “Where is the missing small key?” and “How do I get into the hole under the central platform?”
- Stand over the opening once the platform has risen.
- Equip the Iron Boots and sink into the hole.
- Activate the crystal switch inside.
- Defeat the enemies released from above.
- Remove the Iron Boots, float back up and open the chest for the small key.
Players who skip this hole usually reach a later locked door with one key missing and then backtrack through rooms unnecessarily. The key is not in a random side room; it is tied specifically to the middle-water position of the central platform. On 3DS, the camera cue makes the opening easier to notice, but the action is the same: wait for the platform to rise, sink through the opening and trigger the switch.
If you fall beside the opening, rise, reposition over the hole and try again. Do not change the water back to low simply because the first drop was missed; the platform and its opening are meant to be used at the middle setting.
Collect the additional key and compass
Bomb the cracked wall at low water
Lower the water again and revisit the room where you first found Ruto. Bomb the cracked wall to reveal another small key. This revisit is intentional: the wall cannot be used as part of the initial flooded route.
Keep this key separate in your notes from the key under the central platform. Both are easy to confuse when a later locked door asks for more keys, but they come from different water settings and different rooms.
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Take the Compass in the east-side spike room
Raise the water to the middle level and enter the east-side spike room. The route leads to the Compass. Its crystal switch is timed, so position yourself near the chest or use a projectile to activate the switch from a useful position. The exact switch-side interaction differs between editions; if the switch appears on the opposite side of the gate from the instruction you expected, use the layout shown by your version rather than forcing the Nintendo 64 or 3DS method.
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The Compass is not the same progression check as a small key. If you have the Compass but a door still refuses to open, return to your key ledger and verify the water setting instead of assuming the chest was the required item.
Raise the water to its highest level
From the middle-water routes, use the west-side path and its water spout to reach the third Triforce mark. Play Zelda’s Lullaby there to raise the water to its highest setting.
Before leaving the control room, note your return route. The highest setting opens upper passages, but it does not make every route back to the tower available. The safest habit remains the same: after changing the level, return to the central chamber and inspect the newly raised or submerged routes.
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Take the high-water east passage
At high water, traverse the east passage and move the block as indicated by the route. Then return to the west-side locked door. The path continues through moving platforms and a water-control room.
Trigger the Dark Link encounter
In the illusion-like room, approach the far door. When you reach it, turn around to trigger the Dark Link encounter. Defeat Dark Link, then open the chest for the Longshot.
The Longshot is the temple’s major progression item. It reaches targets and gaps that the ordinary Hookshot cannot, so several earlier-looking dead ends become valid routes only after this fight. If a target appears too far away, mark it mentally and return after collecting the Longshot instead of assuming the room is optional.
Do not search for the Longshot in a side chest before the Dark Link fight. The encounter and chest are a paired progression step: reach the far door, turn around, win the battle, then open the reward chest.
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With the Longshot, revisit the temple’s side passages. Lower and raise the water as required; high water is not automatically the correct setting for every late route.
- Use the Longshot to cross gaps and reach distant targets.
- Re-check doors that were blocked by water or positioned beyond the Hookshot’s range.
- Collect the remaining small keys before attempting the Boss Key route.
- When a passage seems to end, ask whether its target is reachable only with the Longshot or whether the water is at the wrong level.
Navigate the boulder-and-vortex route
One late route combines moving boulders with whirlpools. Stay clear of the vortex centers and time each movement around the boulders. Do not let the current carry you into a whirlpool while you are waiting for a safe opening. Continue through the route until you reach the Boss Key chest.
In this section, patience is part of the puzzle. Watch one boulder pass, identify the safe line, then move across rather than correcting in the middle of a current. If the route seems impossible, verify that the Longshot is equipped and that you have not entered from a water level that leaves the intended target out of reach.
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Collect the Boss Key before the boss door
The Boss Key is a separate late-game pickup, not an automatic reward for obtaining the Longshot. Open its chest, then return to the central chamber and restore the water level needed to access the north-side boss route. If the boss door is still unreachable, the likely cause is a water setting or a missed return to the hub, not a missing combat item.
Reach Morpha’s room
Use the Longshot on the large dragon target on the north side of the central chamber. This carries Link to the boss door once the required water level and Boss Key are in place.
That target is a final route check. If you can see it but cannot connect, check three things in order: the Boss Key is in your inventory, the water is at the level required by the north-side route, and the Longshot rather than the ordinary Hookshot is equipped.
Defeat Morpha
- Stay on the surrounding ledge instead of standing in the water.
- Watch for the exposed nucleus inside the moving water mass.
- Use the Longshot to pull the nucleus out of the water.
- Strike the exposed nucleus with the sword.
- Keep your distance from the water tentacles so they have fewer opportunities to grab Link.
The fight rewards the same positioning discipline used in the dungeon: control where you stand, wait for a safe opening, then use the correct tool. The ledge gives you room to react while the Longshot creates the attack opportunity. If a tentacle closes in, retreat along the ledge rather than chasing the nucleus into the pool.
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“How do I change the water level?”
Find a Triforce mark and play Zelda’s Lullaby. The lowest, middle and highest settings are controlled by three different marks. If you cannot find the next one, return to the central chamber and use the locked or newly exposed route at your current level.
“Where is the missing small key?”
Raise the water to the middle level at the second Triforce mark. Sink through the hole beneath the floating central platform, activate the crystal switch, defeat the enemies released above, and float up to the chest.
“How do I get into the hole under the central platform?”
Make sure the water is at the middle setting, then wait for the platform to rise. The opening is directly beneath it. Equip the Iron Boots while standing over the opening, sink down, activate the crystal switch and remove the boots to float back to the chest.
“Why can’t I reach a target?”
Check whether you have defeated Dark Link and collected the Longshot. Later targets and gaps are deliberately beyond ordinary Hookshot range. If you already have the Longshot, check the water level before concluding that the target is decorative.
“The route I used before is blocked.”
Water-level changes alter access in both directions. Return to the hub, inspect underwater openings and newly raised ledges, and do not assume the route that worked at high water also works on the way back.
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Confirm your edition. The Nintendo 64 and 3DS versions place one described switch differently, and the remake’s visual cues can make the intended approach clearer. Follow the switch position you can actually see rather than repeating an action designed for the other version.
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“I have the Longshot, but the Boss Key route still stops.”
Revisit the water controls and cycle through the levels deliberately. The Longshot opens targets and gaps, but it does not replace the water-level requirement for every room. Confirm that the remaining small keys are collected, then use the boulder-and-vortex route to reach the Boss Key chest.
“Can I go straight to Morpha after Dark Link?”
No. Dark Link gives you the Longshot, but the Boss Key is a separate pickup. Finish the remaining side routes, collect the Boss Key, restore the water level needed by the north-side route and then use the Longshot on the large dragon target.
A compact completion checklist
- Identify whether you are playing Nintendo 64 or Nintendo 3DS.
- Find the first Triforce mark and drain the temple.
- Get the map after meeting Ruto.
- Open the torch door and take the first low-water key.
- Clear the drained hub and spinning-water route for another key.
- Raise the water to middle and collect the key under the central platform.
- Bomb the cracked wall in Ruto’s room for the additional key.
- Collect the Compass in the middle-water east-side spike room.
- Reach the third Triforce mark and raise the water fully.
- Defeat Dark Link and take the Longshot.
- Use the Longshot while revisiting routes at the water levels they require.
- Survive the boulder-and-vortex route and collect the Boss Key.
- Restore the required water level and Longshot to the dragon target.
- Enter Morpha’s room and attack from the surrounding ledge.
Frequently Asked Questions
What is the most important Water Temple rule?
Treat the central chamber as a hub and the water level as the route selector. After every change at a Triforce mark, return to the hub and inspect doors, ledges and openings again.
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The middle level. When the central platform rises, sink through the opening beneath it with the Iron Boots, activate the crystal switch, defeat the released enemies and float up to the chest.
Is the Water Temple route different on Nintendo 64 and 3DS?
The major layout and item progression are the same. The 3DS remake makes Iron Boots switching faster and adds visual route cues, while at least one crystal-switch interaction places the switch differently.
When do I get the Longshot?
After reaching the illusion-like room at high water, approach the far door, turn around to trigger Dark Link, defeat him and open the chest.
Do I need the Boss Key before reaching Morpha?
Yes. The Boss Key is a separate late pickup. Collect it, restore the water level needed for the north route and use the Longshot on the large dragon target.
What should I do if a room seems to lead nowhere?
Check the water setting and your equipment. The passage may be underwater, too high to reach or waiting for the Longshot. Return to the central chamber before trying another route.
The Bottom Line
Change the water only at a Triforce mark, then return to the central chamber and reassess the routes. Clear the low-water rooms, take the key beneath the middle-water platform, raise the level for Dark Link and the Longshot, then revisit the temple for the remaining keys and Boss Key. With the correct water setting, the right boots and a deliberate hub reset, the Water Temple becomes a sequence of readable route changes rather than a maze.
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