You can warp to the Water Temple during Death Hole WW by entering the boss room of the Forest Temple or by reaching Ganondorf's room. You then have to savewarp if you want to finish the dungeon.
There are three ways to dive to Ruto on OoT3D without the Iron Boots: Spell Diving, Bottle Diving and Hookshot Jumping.
By using a spell such as Din's Fire, you can time a tektite to knock you off the ledge during the cutscene and reach Ruto.
If you catch either Bottled Fish or Bugs while in the air with Hover Boots, you will fall during the cutscene. You can then swim to reach Ruto.
With Hookshot Clipping you can reach three keys early: the one on the second floor where you first lower the water, the one in the block push area, and the one in the square area with the current and dragon statues.
By doing a Hammerslide, Hoverboost, Hoverslide, hoverflip, or Hookshot jump, you can cross the gap without needing the Longshot.
By doing a Hoverboost, Hammerslide, or a Hookshot Jump into the unloaded room, it is possible to skip raising the water.
With a very precise Megaflip + Damage Boost, it is possible to get into the current room with the Tektites and the boulders to get this Gold Skulltula
Doing an Entrance Point glitch to the other room, then doing a Hookshot Clip into the weird collision lets you skip the song of time block.