This Zelda: Ocarina of Time 3DS Water Temple walkthrough will help you through this difficult dungeon.
The Water Temple was made famous in the original Ocarina of Time due to the cumbersome nature of the Iron Boots and how you had to press Start and navigate to the Equipment Subscreen each time you wanted to take the Boots on or off. You have to put the Iron Boots on to sink into the water, and take them off to float back to the top.
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This was very annoying and took away from the excellent design, layout and tough puzzle solving that the excellent Water Temple showcased. You can see exactly what I mean in this walkthrough of The Legend of Zelda: Ocarina of Time N64’s Water Temple.
Thankfully Nintendo’s Zelda producer Eiji Aonuma first order of business with Zelda: Ocarina of Time 3D was streamlining the way the Water Temple works! They did this by removing boots as an Equipment item and giving them as a normal item, which you can then put on or take off using either a button on the 3DS or a slot on the touchscreen. Genius!