See Morpha for the boss fight in Water Temple.
Notes:
The video below also contains a slower ESS-less setup.
To the left of the entrance there is a small piece of land that is part of the large island you can stand on. Get on it and go as far submerged as possible without swimming. Now aim the hookshot and try to hit the crystal. Its difficult to hit because not much is in view but if you just try moving around a little bit you can get it. Then just dive into the temple if you have golden scale, and if you don't you can ocarina dive in.
Due to the water covering most of the map out of bounds and the exact arrangement of the geometry of the main island, it's possible to swim to the Water Temple load zone out of bounds. As shown in the video, it's useful to swim nearly in bounds to get the camera to follow Link closely again. In addition to the setup below from Zora's Domain, this can be done by clipping into Lakeside Laboratory.
See 6:27 in video.
See 8:30 in video.
You must not have any strength upgrade (goron bracelet/silver or gold gauntlets) or this will not work. With a piece of grass in the patch closest to the lab house, place a bomb far enough so that it wont destroy the piece of grass you will use for a superslide but will hit your shield when standing right next to the piece of grass. Look behind you and make sure you have an angle that will not make you fall off the nearby ledge. Now do a superslide with a piece of grass, making sure the bomb doesn't destroy it. When you have gone down the slope about 1 Link height, let go of R and you will teleport to the piece of grass, but under it, and you will fall into OoB water. From there just navigate to the Water temple entrance.
On the island containing the Water Temple entrance, there is a narrow brown/gray ring. Stand on this ring and face the platform where you would normally obtain the Fire Arrows. Turn around, and shield drop a bomb on the brown/gray ring and back up out of the the bomb's "grab" range. Do a megaflip, and hold back --towards the Fire Arrow platform-- on the control stick. You should hit the ground in front of the platform and clip OoB. From here, simply swim above the loading zone to get into the Water Temple.
The longshot can be skipped by crossing the gap leading to the door. There are multiple methods, but these are the most useful.
This is the fastest way to get to the boss door from the dungeon entrance if hover boots are available. Start the HESS with left ESS, then switch to right or down-right ESS after pausing to equip the hover boots. Try not to run into the wall, but also avoid running into the tektite because it can randomly attack. After Link passes the tektite, target it for a good angle. Let the targeting break automatically when Link leaves the tektite's range, then release the control stick to neutral for at least one frame before starting to hold down to reach the ledge.
One cue not mentioned in the video below is to do with recognizing a first frame dive without buffering the dive input. If you buffer the recoil and pause on the first recoil frame (which only works with a first frame dive), then if the explosion's color is still the lighter orange and hasn't started changing to darker orange, that means you got a first frame dive and can continue on for the popup from there.
If you have an equip to do and pause buffer the chu drop + backwalk input, it’ll change the frame data slightly from what's shown in the video such that the first 2 dive frames have the same A release leniency (1st/2nd recoil) rather than the last 2, which makes it safer to use recoil frame 1 if you’re mashing A trying to dive as soon as possible. This does not work with the second setup shown.
Do four contortion hovers then backflip to cross the gap. Alternative hovering options include: sideflip hovers, slingshot hovers, hover boots hovers, angled backflip hovers.
Get on the middle platform and face the boss door ledge. Turn around and get against the wall. Strike the wall with the Megaton Hammer and then pause. You are looking for the frame where the point on the back of the hammer is right next to Link's head. Now equip the hover boots and unpause. Simply run forward and grab the ledge.
Initiate a superslide then equip the hover boots. When you start to hover, let go of R and hold down to grab the edge.
With Kokiri boots, sidehop right immediately after entering the room, then turn around and backwalk. If you were quick enough and kept Link facing cardinal directions, he won't hit any blade traps. A slower alternative that may appeal to beginners is running up the left side of the slope. Link can roll up the slope with hover boots on, but not with Kokiri boots.
This ground clip requires Link to take damage on the frame he automatically falls from a hover near the ground. This setup makes the ground clip lenient because the bombs are placed such that the first bomb's explosion detonates the second bomb, which then hits Link on the correct frame. This means that the backflip to hover is frame perfect, but the timing for dropping the second bomb doesn't matter at all.
In steps 3 and 4, Link needs to drop both bombs to his side. This means pressing shield on the same frame as bomb or on either of the two following frames. Also, when turning in step 4, be careful not to hold shield while not targeting, as this will cause Link to crouch and lose ISG.
This is similar to the strat above but doesn't begin from Link's position after getting ISG, making it a good backup if you are retrying the trick and still have ISG.
In the room where you can lower the water level to the first floor, there is a bombable wall on the second floor that contains a key. Normally you would have to raise the water to the second floor to reach it, but it can be reached by side-jumping into the corner, then using a jump attack to land on the ledge, or with a gainer (recommended).
Backwalking and dropping from the ledge is 0.3s faster than jumping down and puts Link right next to the torch.
The most important thing is that when you sidehop into a wall and pull out hookshot, it puts Link's arm closer to the wall.
For Dark Link there are two pieces: spawning him quickly, and fighting him.
Target to square the camera at the start of the room, 90deg left, target, walk forward to a bit before the end of the beige stone (not precise), then just sidehop right 11 times
His health is directly proportional to your max health. 1 heart container = 1 Master Sword swing. For AMQ, the best strat is to keep your bearing from those 11 initial sidehops, and do right sideslashes to catch him with the sword over the back of Link's left shoulder. That basically amounts to just strafing a bit right to get him to your left before slashing. He keeps spawning behind you so every time he approaches just strafe right a bit then slash. You can do a sidehop in between each hit to make it so you arrive at the door perfectly after the 6th hit (ideally AMQ runs have 6 hearts here).
If he stops behaving as you want (sometimes he decides to be an annoying acrobat jumping around everywhere), try intentionally baiting him with a vertical slash to get him slash you from behind to damage you. That settles him down (total vibes based info, dunno how to explain it better).
Don't go too close to the exit door before the final hit or he will run away from you. Just barely onto the beige stone is as far as you should go. 1 sidehop with a little right strafe for each of the 6 hits should space you just right anyway.
Notes:
In the room with the spikes blocking your passage to the Boss Key, you can get past them without the longshot.
With a well timed backflip near the end of the hover you can land on top the spikes.
Hover along the wall to get past the spikes.
This requires the iron boots and the hookshot. Use the torch on the bottom floor to clip out of bounds then swim to under the platform that leads to the boss door. Swim off the edge and jumpslash to land on top of the spikes.
You can get into the doors on the second and third floor of the Water Temple without raising the water level. Perform a Hover Boost in the direction of one of the doors and right when the hover is about to end, you should be just in front of the door. If you look carefully in the video, you can see the A button very briefly reads "Open".
If you want to return to the top without savewarping but the water level is too low, you can use the pool of water at the dungeon entrance to float back up. Just torch clip to get out of bounds, then swim to the water at the entrance.
Recoil off the door and equip hover boots, hold left until the door closes, Grab the Longshot and weirdshot under the chest to void out. Hold down and jumpslash to the floor below and hookshot back up to skip it.
Beat Dodongo's Cavern without getting the bomb bag. Before you pull the Master Sword, go Bombchu Bowling and win the Big Bomb Bag. Now go back to Dodongo's Cavern as adult and obtain the Bomb Bag. This will put a Bomb Bag over your Bombchu slot.
Alternatively, you can also use DoT Skip to get around having to beat Dodongo's Cavern. You can then RBA Cojiro to modify your left side equipment with 2 bomb bags. Now simply open the bomb bag chest in Dodongo's Cavern as an adult to get the equipable bomb bag. Note: You must have a bomb bag in your inventory to get this equipable bomb bag; simply skipping the one in DC and going back to get it as an adult will not work.
Now go to the Water Temple with a Bottle on B and the Bomb Bag you now have on C-Right. Now if you empty or put an item in the B Bottle, you'll receive a number of Water Temple Small Keys equal to the hex value of your B Bottle. See Reverse Bottle Adventure for more information.