You should have 2 keys now.  Go to the tower in the middle of the main room and find the locked door and go through it.  Use your hook shot to go up to the ledge above you then play Zelda's Lullaby in front of the Triforce symbol to raise the water level.  Now put on your Iron Boots and drop back down.  Underneath where the block was is now a hole.  Drop down and follow this corridor and you'll end up in a room with a shock switch.  Hit it with your hookshot from a distance and back away as a bunch of baddies drop down from the ceiling.  Here's a battle tip for you.  Z target the rock thing (the thing that turns into a spiked ball when you get to close) and hit it with your hookshot to kill it and it won't even be able to attack you.  If it does come at you, block it with your shield and it will turn back into a rock thing.  Walk around Z targeting all the rock things and kill them and you'll be left with two clams.  Kill them using the hookshot method you used before.  Once they are all dead a grate on the other side of the room will open in the ceiling.  Float up there to get another key.  Go back to the tower room and go through the upper door.

Walk around until you see a tunnel with two pots in front of it and go in there.  Follow the passage, use your hookshot to get over the spikes, then use your hookshot again on the ceiling to get up in the room.  Go stand next to the treasure chest and shoot an arrow at the shock switch.  Then get the compass.  Go back out to the main room.  Jump in the water, put on your boots, and sink to the bottom.  Walk into the room where you met Ruto (the one with the torches on either side of the entrance) and float up.  Blow open the crack in the wall to get your third key.  Now go back into the main room, unequip your boots and swim left across the wall.  Enter the first locked door you see.  Go stand on the water geyser and then shoot an arrow at the shock switch to have it shoot you up to the next room (you can also use a bomb if you are out of arrows).  Go through the door and you're at the high water level Triforce mark.  Play Zelda' Lullaby to raise the water level to it's highest point. 

Now drop into the water and swim left to a locked door and go through it.  Hop down two platforms and this platform will move.  When it's at it's lowest point jump to the non-moving platform to your right.  Now use your hookshot on the hookshot targets on the fronts of the moving platforms to make your way up to the top of the waterfall and go through the locked door.  Now your in the water level puzzle room.  If you mess up at any part of this room and fall in and the water level is low, use your iron boots to sink to the bottom then use the hookshot to hit the shock switch and raise the water level, then float up and climb back on to the starting platform to start over.

Use your hookshot on the shock switch in the middle of the room to raise the water, then hookshot over to the statue nearest you.  Now shoot the switch again with the hookshot and the water will lower.  Walk to the back corner of this platform and look to your right.  Use the hookshot on the hookshot target on the wall to get over to the next platform.  Climb over the statue head and walk to the edge and shoot the switch again to raise the water again.  Now hookshot to the next statue and hit the switch once again to lower the water.