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by ABXInferno

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FAQ/Walkthrough by ABXInferno

Version: Zelda | Updated: 01/13/18

Master Quest Dungeons

Water Temple Master Quest


Heart ContainersPieces of HeartGold SkulltulasOcarina Songs

Learn more about getting here in the main walkthrough.

Ah, the Water Temple. The most infamous Ocarina of Time dungeon that conjures up bad memories left and right, for kids all over the world. The dungeon so bad Eiji Aonuma had to apologize for it. And now, in Master Quest? Did they make it even worse? Two things. One, I never found the original version to be that bad. I despised the Great Bay Temple in Majora's Mask more, and even Jabu-Jabu's Belly I disliked more in Ocarina. And two, the Master Quest version, I find, is actually a more pleasing run through than the original. Don't get me wrong: it can be tougher to figure out, but there's not as much back and forth involved.

Anyways, enough blabbering. Step inside and equip the Iron Boots to sink to the lowest level. Enter the door bordered by yellow/green lines to find Princess Ruto... *groan*. De-equip your boots and swim through the crack in the wall. Use your Hookshot to hit the symbol on the wall and reveal a chest. But we can't get it while underwater, so swim to the top and play Zelda's Lullaby next to the symbol to lower the water level. Now stay in the middle of the room and cast Din's Fire to light the torches in the corners of the room. Proceed through the door, where there are three Stalfos waiting to ambush you. Kill them to re-open the door; before leaving, hit the symbol on the wall to spawn the chest containing the Dungeon Map.

Return to the previous room and drop down to the bottom. Light the two torches in the corner and head through the newly-opened door. Clear the room of its enemies to reveal another chest, this one containing the Compass. Return to the previous room, stand on top of the Hookshot target, and look up to the second level for another target. Hookshot up and open the chest for the dungeon item - the Longshot! It's an upgraded Hookshot that lets you shoot even further. You get this item here way earlier than you would in the original version. And also, I will continue to refer to it as the Hookshot, because they're essentially the same item, just upgraded.

Drop down and exit back to the central chamber. Enter the red door that is now accessible to us and Hookshot up to the second level. Play Zelda's Lullaby to raise the water level to the second floor. Exit the door and head to the opposite side of the central chamber where there is a yellow switch on the opposite side. Step on it and proceed through the newly-opened passageway. Head to the end and cast Din's Fire to light the torch on the opposite side of the grates and open it. Destroy the crates to find Gold Skulltula #72.

On the left side, there is a large room with crates to refill your stock of hearts and arrows if you need. Head down the right path and Hookshot up to the target. Step on the switch and exit back to the central chamber. Hop down to the second floor and head into the passageway with the spikes. Hookshot up to the ledge, and towards the ceiling. Grab one of the small crates, drop back down and head back into the central chamber. Cross the pit towards the center ledge and drop it on the pressure switch on the opposite side. Head through this door.

Next to the door, destroy the crate to find a crystal switch. Hit it, defeat the Lizalfos and Hookshot up to the higher level. Destroy the nearby crates to find Gold Skulltula #73. Exit the door and play Zelda's Lullaby to raise the water level. Drop down to the second floor and enter the red door. Surface and swim up onto the platform here. Play the Song of Time to spawn a time block. Clamber atop it and cast Din's Fire again to light the four torches in the corner to open a grate into the basement. Drop down towards it.

Here, destroy the crates to reveal a crystal switch, which does nothing really. Head to the back of the passage and step onto the blocks to have them sink, revealing another crystal switch. Activate this one, then swim towards the grate it opens. Hit the symbol on the wall to spawn the chest containing a Small Key. Return to the central chamber, swim up towards the surface and open the locked door to the east.

Drop down onto the moving platform below. Look above the doorway we entered through for a crystal switch. Hookshot it to activate it, then aim your Hookshot at the top-right target, the only one with another platform below it. Hookshot the symbol on the wall, then grapple towards the newly raised target on the doorway. Enter the door and drop down. Kill the 3 Stalfos here before Hookshotting back up towards the entrance. Grapple across to the new target, and then the one on the wall. Climb over the half-raised statue head. Turn the corner and smash the jars for a free Fairy before grappling across. Leap over to the narrow pillar in the middle and grapple up towards the target on the ledge above. Proceed through the door for the dungeon miniboss.

In this room, proceed to the opposite end and turn backwards to find... your shadow? This is Dark Link! He is damn good at blocking your attacks. Want an easy way to kill him? Equip the Megaton Hammer and just keep pounding at him. Another easy way to dispose of him is using Din's Fire, which always hits. Otherwise, if you feel like fighting fair, just L-Target him and attack when you see a chance, that's all. After quite a few hits, he will go down. The illusion of a room fades. Head through the door to the next room, which is where you would get the Longshot in the normal game.

Anyway, hit the symbol on the wal and drop down into the room below. Cross this sort-of river by Hookshotting across the targets. As you turn the corner, look to the wall above to find Gold Skulltula #74. Make your way to the end and drop down into the room below. Swim through the opening in the water. Make it to the end of the passage towards a small room above the water and cast Din's Fire to open the door back in the earlier section. Use it.

In the next room, drop down onto the geyser and activate the crystal switch from here. Standing atop the geyser, cast Din's Fire once more to light the two torches behind the grate, opening the path to the Boss Key. Use the passage behind to return to the central chamber. Head through the northern door in the bottom-most level. Swim up to the surface and grapple past the spikes to the next door. Now, I should note, if you'd like, you can now head straight to the boss chamber, but there are a few collectibles we can grab before then. In this large room, notice that Navi turns green by the corner. Sing the Scacrecrow's Song to make Pierre appear; grapple toward him. Take a mental note of the locked door here before sinking down at the end of the passage. Make your way towards the door at the end of this underwater corridor.

Defeat the Stalfos to re-open the door before destroying all the crates in the room, because inside one of them is a Small Key. Collect it and return to the locked door we saw earlier. Inside, do what we did with the Boss Key door and cast Din's Fire while on the center geyser to light the torches in the room. Head through the door on the opposite side. Here, kill all of the Dodongos, then use the Hookshot to reach the target on the ceiling towards the other door in the room. Open it and destroy the crate in the corner to get Gold Skulltula #75.

Now, if you check the normal dungeon's guide, you will find five Gold Skulltulas in this dungeon, and in the Master Quest dungeon, we have encountered four. For the final Gold Skulltula, we need Fire Arrows, which while you can technically exit the dungeon and get now, is something we will be obtaining very shortly in the main game after this. Look for the typical blue box there to find the final Gold Skulltula, #71, which is in the southern room of the first floor.

With that out of the way, head back to the central chamber and Hookshot to the boss door in the north of the third floor. Hookshot across and enter the door. Inside this final corridor, Hookshot the barely visible crystal switch above the doorway and grapple to the targets that appear. Use your boss key to open the door here.

Boss Battle - Morpha, Giant Aquatic Amoeba

As you enter, Navi will remark the water isn't normal. Cross the pit over to one of the central platforms and the boss will appear! Quickly hop on over to the side and keep an eye out for Morpha's tentacles, which leave you plenty of time to react because they take forever to form properly. Your goal here is to Hookshot his brain/guts and slash at it. Repeat this process through the entire fight. That's all.

Want to do this very quickly? Stand in a corner and grab his guts from there. Keep Hookshotting him as you turn around so that Link is facing the corner, and Morpha's guts are cornered. Just keep stabbing and slashing with your sword, and it will have absolutely no recourse or escape. The fight will be over in seconds.

Having completed the dungeon, grab the Heart Container on your way out, and you will be granted the Water Medallion. With that complete, click here to return to the main walkthrough