Once you enter the aquatic temple, utilize the nearby Bird Statue. Use the ledge you’re to go around the edge of the room, counterclockwise, defeating the Green Chuchus as you go. Eventually, you’ll find a locked door. Jump at the switch on the wall nearby to unlock the door. Go inside.
Here, jump off the ledge onto the lilypads below - note that, when you land on a lilypad from a high distance, you’ll flip it over, bringing the harmful spiky underside aboveground, making it safe to swim underneath. Anyhow, climb up the nearby ledge and slice one web down. Hit the Skulltula with a down-up vertical slice, then use a fatal blow to end it. Repeat with the other spider web and Skulltula.
Further ahead, you’ll come to a door with a weird lock on it. There are four switches you must hit on the lock in a certain order, one that corresponds with a certain riddle in the entrance area. You DON’T have to go back there; you will, however, miss out on some easy-to-find Silver Rupees. If you go back there for the riddle, the two Silver Rupees are on the statue’s hands. Anyhow, the solution to the puzzle lock is: top, bottom, left, right. Those are the four sections of the lock you are to hit with your sword to unlock the door. Once it is unlocked, go on through.
Afterwards, hop across the lilypads to the southeastern corner of the room. There, climb the vines to the empty ledge, then unleash your Hook Beetle, using it to cut down the Skulltulas hanging from the roof, killing them once they hit the water. Next, look down from the ledge, looking at the lilypads, to find a lilypad with larger-than-usual spikes underneath. Flip it over and go through the newly-revealed passage. Continue for a Red Rupee, then spin attack through the blockades further ahead.
In the small room, climb the vinery and go through the door here to find a chest on the other side. Inside, you’ll find a Small Key. Use the nearby water spurt to reach the upper ledge and follow the path to the entrance door and out of the room entirely.
Back in the central room, head back south, towards the entrance, then cross the lilypads to the north. You should eventually land on the ledge around the statue. Go forward to the locked door and unlock it. In the new room, drop to the bottom of the pit below to fight a Stalmaster!
The Stalmaster is little more than a buffed-up Stalfos. It has four arms and four weapons. It will initially fight, however, with only two, so it’ll be like fighting a Stalfos for a bit. Always try to hit the exposed parts of the enemy! Soon, your opponent will use all four arms. Again, continue to hit the exposed portions - the only difference is that you have be more specific on where you strike. I think some hearts were surrounding the room if you need them.
After the battle, go through the newly-opened door to find a chest. Inside, you’ll find a new item, the Whip. Much like the Grappling Hook of Wind Waker, you can use this to latch onto things or to steal items from enemies. Exit the room and use the Whip on the water valve on the other side of the room and turn the valve to create a water geyser. Go into the geyser, then continue to repeat the process to reach the top of the room. Use the Bird Statue and go down a few floors to where you entered through, then exit.
Back in here, go along the edge of the room, counterclockwise and up the ledges to find some branches on the wall. You can lock-on to and Whip them to make a swing of sorts. Use it to cross the gaps ahead. At the other side, open the chest nearby for a Dungeon Map. Get back on the water and head to the west side of the room, where the red X on the map is. There, you’ll find an unreachable wall switch. Whip the lilypad’s spikes to turn it over. Get onto the now-safe lilypad and hit the wall switch with the Whip to activate it, causing the nearby fish head to stop blasting out water.
Anyhow, jump into the water below and swim through the fish head, going west. Surface in the next room and kill the Skulltula. Walk around the path behind the fish head to find a chest with a Red Rupee inside. On the other side, you can find a wall of bars. Behind the bars, you’ll find a wall switch. Vertically swing the Whip to hit the wall switch and open the gate.
Head into the next room and kill the Bokoblin Archer nearby. Continue along the path, defeating the Green Chuchus on the way. Further ahead, you’ll find a grouping of Blessed Butterflies. Play the Goddess Harp to make a Goddess Wall appear! Utilize it, then return to the Bokoblin Archer’s ex-platform. Climb the vinery to the above ledge and, there, dash up the rotating column of vines. Don’t move around much - just jump off when you’re over the platform with a Bokoblin Archer.
Defeat the aforementioned enemy, then look around. You should find an unused set of vines with a Walltula climbing them. Kill it, then use the Whip on the swinging post nearby. Hold B to stop swinging, then turn around and face the wall switch. Swing back and forth a few times to build up momentum, then jump at the wall switch, lowering the bars in the above room. Climb back up the vines nearby, then swing back on the post, but, this time, aim for the vinery leading to the above room from earlier. Climb up and defeat the three Deku Babas you find here. Afterwards, use your Whip on the valve nearby to cause a whirlpool down below. Go down there and jump into it. (Kinda makes you think of that old nursery rhyme, “The Itsy-Bitsy Spider”, doesn’t it?) >_>
After getting sucked through the tunnel, you’ll be on the lowest floor of the dungeon. Get above the water, onto the platforms, and use the Bird Statue nearby. Look to the roof of the room for some Skulltulas; use your Beetle to cut them down. One should end up flipping over a lilypad. Swim through the newly-unblocked tunnel to go forward.
In the next room, you’ll notice a Bokoblin Archer on the right side of the waterway. Get onto the ledge and use your Whip on the Archer to get a Small Key, then proceed to kill the enemy. Across the waterway, you’ll find a locked door, which you can now unlock. Go through.
When you enter, you’ll take a nice, long look at the ominous room down below (you don’t get much worse than skeleton imprints). We’ll be going there in a bit. For now, go over to the Bokoblin Archer and get rid of ’im, then go to the other end of the room. Swim into the pipe to return to the first level of the northern chamber.
Swim to the surface and go north, onto the platform. Jump onto the wall switch to open up some bars, permitting you access to the entrance room. You’ll also find a Bird Statue nearby, so you might want to use it. Get into the water and spin jump onto the dry platform nearby. Afterwards, you should be able to find some vines nearby, on a wall above you, with a lilypad below it. Flip the lilypad with your Whip, then get rid of the Walltula with the Slingshot. Get onto the lilypad and climb the vinery. Follow the path to and defeat the Quadro Baba. Go to the edge of the platform and jump off to flip another lilypad.
Go into the newly-revealed passage, grabbing the Red Rupee on your way, then avoid the Froaks. (Killing them is out of the question; the explosion is likely to hurt you.) Once you reach the end of the tunnel, surface and go upstairs. Defeat the Deku Baba hanging from the ceiling, then Whip the valve to create a geyser where the lilypad was (the one you flipped). Get back into the water and go across the room to the vines from earlier. Climb them and go along the path. At the end, flip the lilypad over with your Whip, then safely jump to the other side. Go upstairs and you’ll find an out-of-reach wall switch; smack it with your Whip to trigger it. Proceed through the newly-opened doorway.
Hey, I think we know this room! Anyhow, go to the right and you’ll notice some vines. Don’t climb them yet – shoot down the Walltulas on them with the Slingshot, then start climbing to the left. At the far left portion, drop off the vines to find some more. Continue climbing leftward to a new ledge. There, drop off of the vines and use the Whip to make a geyser appear. Go ahead some more to find a large switch on the wall – use the Whip to pull it down, thereby causing the giant statue nearby to sink down a floor.
Jump into the water and head to the southern side of the statue. Get onto the ledge and go through the door. There, drop to the bottom of the statue, using the Sailcloth to soften the fall. Go through the door down here for a new area. Be wary in here. You’ll find a lot of Cursed Bokoblins here. They can Curse (prevent item usage) you and are only killed with fatal blows (a spin attack is most effective in creating the proper situation). They are also scared when they see your Sacred Shield (or an upgrade?) raised.
Get rid of the local Cursed Bokoblins, then follow the path to the side of the door to find some more. You see that purplish water nearby? Stepping in that will Curse you and can often hurt you. Anyhow, go to the (rotting) lilypads. Cross them quickly; have your Whip at the ready to flip the last one. (I need to emphasize speed here - those will fall into the cursed water if you stand on them too long.)
Hop across to the solid platform and look to the right. You’ll find a huge skull spewing out cursed water. You can send the Hook Beetle through one of the skull’s eyes to find a tunnel; hit the crystal at the end to stop the flow of cursed water. Go back across the lilypads and go left at the solid land. Go ahead and defeat the Fire Keese, then, nearby, you should find a bunch of Blessed Butterflies. Play the harp nearby for a Goddess Wall.
Continue along the path to the Bomb Flower. Use the Hook Beetle to take one through the skull’s mouth to a cracked rock further ahead, on a ledge, to Bomb it and get rid of it. Go back around and re-cross the lilypads. Go to the Bombed ledge by swinging to it from the post above using the Whip, then go further forward to the rotating column.
Climb the vines on it, then dash to the apex, then dash and jump to the next column. Hang onto this one as you pass the ledges. Ignore the first one; just jump onto the second one. Follow the path you’re on to the end and you can (and should) dash to the non-moving column. Climb to the ledge above and go ahead to a switch. Use the Whip to pull this switch to the left, reversing the direction of the rotating columns.
Jump onto that same ledge, then go uphill and defeat some Cursed Bokoblin as you ascend. At the top, jump onto the next rotating column and hang on until you bang into the wall. Follow this path and another non-moving column; climb up those vines. You should see the switch from earlier nearby; use your Whip to pull it to the right. Return to the previous vine column and ride to the end to fall on a new pathway. Go uphill to a high ledge overlooking an empty room. Needless to say, I hope Link doesn’t have acrophobia.
Anyhow, drop into the aforementioned room and approach the rope dangling from far above. Grab it and – I kinda enjoyed how Nintendo thought of this – some Cursed Bokoblins will start climbing after you. You can go down and fight them (I very much recommend doing this for a while with some Treasure Medals – you can farm large numbers of Evil Crystals this way), and/or continue climbing to the next area. If you’re grabbed while climbing up, shake off the enemy and climb some more.
In the next area, utilize the Bird Statue, then jump at the nearby wall switch, causing a ledge to make it easier to hit the large level from earlier. In fact, since we’re here, Whip it back upwards and drop back into the basement from whence you came!
Enter the nearby unvisited room this time. Go forward some to find a valve; Whip it to make a water spurt appear. Go into the room below and snatch the Amber Relic nearby. Then go towards the chest you saw a while ago. Open it to find the boss key for this dungeon, the Blessed Island. Then a bunch of Cursed Bokoblin will appear and the above statue will start sinking. You know what…? Just run back out of the small indentation on the ground and squish all of the Cursed Bokoblin will be nice and flat, although you don’t get any rewards.
Once the statue hits the ground, go into it and start making your way to the top of the statue via the water geysers. You may need to Whip some of the valves if you didn’t do as such earlier when you where here. Anyhow, at the top, use the Bird Statue and insert the Blessed Idol into the lock.
After a short scene, go to the top of the statue and go around, using the Whip to trigger the four valves, causing the statue to rise even further. In the next room, go around and collect some hearts if you need (and maybe an Amber Relic somewhere?), then save at the Bird Statue. Go into the next room for your next cutscene and your next boss.
During the first phase of the battle, the boss is immobile for the most part. It initially attacks by swinging arms at you. Dodge the attack and pull out your Whip, using it to hit the valve on its unarmed arm. Repeat this with the other arm.
Once you do, the boss’s chest will be open to damage. During this time, the axes from two of the arms are thrown at you, and the other arms try to slam you like the other two before it. Run to the weak point and start slicing. After a period of time, you’ll repeat the process thus far until you deal a certain amount of damage.
The boss then enters its second phase. Koloktos becomes mobile, walking around with some giant legs and also wielding six swords (the weak point is guarded by a cage, now). During the boss’s slicing rampage, stay a fair distance back. Eventually, though, three arms will slam down. Unfasten the valves on one arm with the Whip, then pick up the dropped sword. If possible, slice the boss’s torso in a horizontal manner, then hit the cage two/three times, opening up the weak point. You may want to drop the sword now and use your own sword to do damage (it slices faster). You’ll soon have to repeat this process until the boss is defeated.
Update: Thanks to user ABXInferno, there is something you must know about fighting the arms. They only come down to slam at you when you are in the pillar circle. Thanks for telling me this!
After the battle, snatch up the Heart Container and go through the door on the other side of the room. In the next room, go forward and hit the crest with a Skyward Strike. You’ll end up purifying your Goddess Sword with Farore’s flame, transforming it into the Goddess Longsword, which can deal double the previous amount of damage. Fi will then tell you that you ought to return to the Isle of Songs, then you’ll be teleported outside.