This is a little tricky. First go one space south of the Big Chest and face the right. Use the Hookshot to drag yourself over to the skulls, a key is under one of them. Now, go back up and stand exactly one space north of the Big Chest. Make sure you do not fall into the shallow water. Use the Hookshot to drag yourself over to the skulls. Use the key to go inside. In here is a door to the left that can only be opened by standing on the switch under the skull in the upper left corner. Move the statue near the switch over on top of it. Push it to the left so it's along the wall, then push from the below it, upward onto the switch. This opens both doors, you will want to go through the one to the right because they both lead to stairways but the one on the right allows you to flip a switch to drain water in the next room. There are chests in the room southeast of you containing rupees. Go through the door north of where you came.
The next room has several waterfalls and a door. The door leads to a dead end where there are some skulls in a corner and an opening in the wall for Pirogusus to enter. If you wait long enough, more than half a dozen Pirogusus will enter the room one by one. If this happens you're cornered and have to defeat them or risk getting defeated yourself trying to walk past them all. You'll have to go back into the waterfall room. Now what? The map should show you that there is, in fact, another exit in this room. Use the map, press the X button and match up your location with the exit's. Or you can just look at the screenshot below. You can walk under one of the waterfalls, the one second from the right to be exact. Now go through to the next room and go upstairs.
Defeat the Zols and Buris along the way. You're almost there! Get the key from under the skull on the far right, then jump back in the water. There's a current here so be careful. It is possible for the Hovers to catch you and you not be able to swim away in time due to the current. If the Hovers are in the way, cast Ether, Quake, or Bombos to defeat them before jumping in the water. Climb out using the ladder in the middle. Bomb open the wall. The skulls in the next room have some hearts and other items underneath if you need them. If not, use the key on the locked door above the ladder on the left. It leads to a door with an evil looking icon on the floor just in front of it. Boss battle time! Go inside the next room and there is a boss monster waiting for you.