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.
There is also another way to enter Water Temple without iron Boots or hookshot. Go to the house near the lake. Go to one of the corners and try to get as luch of links face in the house as possible without being pushed out then turn around and backflip. If you were far enough in you will be inside the house. In front of the door there is ground missing so you can jumop OoB. From there swim to under the island where the water temple entrance is and navigate for the loading zone. The loading zone extends all the way up to the surface of the water so theres no need to dive.
There is another, easier and faster way to get OoB with a superslide teleport off grass. 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.
In the Water Temple, there are obviously many places where you would normally be required to use the iron boots. However, in many of these locations you can use spell, navi, or bottle dive to reach the desired destination. In some locations, you can simply use a jumpslash or rapid descent in order to dive deep enough.