In a segmented run, normally you would save at one of two points after raising the Tower of the Gods: either inside the dungeon, or outside of it. When saving inside the dungeon, you have to watch the initial cutscene before you can save. This cutscene lasts approximately 9 seconds. When you reopen the file, the water level will have been reset and you'll have to wait for the water level to rise once you've swam over to the platform on the right. However, if you save outside then dungeon, those 9 seconds spent watching the initial cutscene are also spent waiting on the water level. You'll notice that now when you swim over to the right, that the water level will rise before you get to the platform.
With some Tower of Gods doorways, you can clip past the wall the door is in.
To perform the clip, position Link atop the door, to the far right side. Face the wall diagonally to the left, then backwalk off the door. To keep from aligning perpendicular to the wall L target from first person view. Keeping L held down the entire time, climb back up then repeat about 2 times. When you climb up and get pushed into the wall it worked. Careful as you are not far from being ejected back in bounds. The better the initial positioning, the fewer iterations needed, almost all the time 3 will do it.
The main speedrunning use as a glitch where you glide behind the main room's waterfall and get ejected into the tunnel during high tide.
Method 1 (Unreal): To perform this, get a statue and throw it to the corner. Get on the top of the pillar and "fall" off the pillar and you should be holding on the ledge. Wait a second and you should be pulled out of bounds.
Method 2 (Kazooie): From the entrance, go right onto the ledge. Hop onto the pillar near the hut where you place the statue, then Deku Leaf over on top of the hut. Climb to the peak of it, and wait until the water is about to rise. Facing the entrance with water pouring out of it, backflip and pull out the Deku Leaf immediately. Glide over through the waterfall, and release the Deku Leaf when you're up against the front of the entrance when the water is raised. If done right, you'll be sucked inside.
Using a slow superswim, it is possible to simply climb the ledge behind the waterfall, skipping the beginning of the temple. This is most useful in a TAS.
After placing statues on the right and middle switches, roll over the left switch, and you will land of the rising platform as the cutscene begins.
After you picked up the second statue on the first floor, you are supposed to use the Command Melody to jump him over a bridge you get from standing on a switch. Instead of doing this, you can walk with the statue to the ledge on the same side as the switch. Walk up to the pillar which stops you from continue. Walk slowly until Link's left foot is in the air (and a few more pixels) and focus. Change the view until the left side of the screen is at the edge of the right eye of the statue in front of you. Drop focus and move your stick to the right until link has turned 90 degrees. Focus, and sidehop. Continue as normal.
Simply glide to the rising platform and jump to the small key chest. To get back to the door quicker, jump into the abyss and you will death warp back to the door.
Place one statue on either of the scales. Jump off the ledge by the opposite scale and glide to the scale's far edge with the deku leaf. Fall, roll, and grab the ledge of the platform. It is also possible to get to the ledge using only leaf pumping, but it is more difficult.
Put two statues on one of the two scales. On the opposite scale, while holding the goddess statue, sidehop back and forth until the scale reachs the appropriate level, then proceed to the next room.
Get on the block in the middle of the room and glide to the golden ledge on the left side of the lasers. From here, glide and grab the ledge of the statue. "Call" the goddess statue, then immediately glide back over the lasers.
Instead of climbing up the ladder and grappling to the clapper of the bell, you can skip climbing the ladder all together. Get up against the ladder without climbing it and pull out the Grappling Hook. Aim it at the bottom of the bell platform until the yellow targeting symbol appears. Now just grapple to the bell.