Fortress of Female Pirates
As Zora Link, explore the underwater area of the first map of Great Bay. Head all the way to the right, and there should be wooden boards against the rock wall with the skull and crossbones symbol on them. Crash through these and reveal a hidden passage to what appears to be the pirate's hideout.

There will be several pirates patrolling the area outside the fortress in boards. If one spots you, you will be thrown out, just like the Deku maze. Try to sneak against a wall and jump down into the water as Zora Link. Find the vent in the fort that shoots currents of water to push you back, then walk up the orange metal pathway by there. Follow that path, careful not to be spoted when you surface, and jump on the switch as Goron Link. The green grate underwater on the other side will open. Jump back down and enter through there.

Follow the corridor and you will get to a mini underwater maze. Break the wooden boards when you have to, and push/pull the blocks to get through. Not very tough. Swim to the switch that is shooting jets of water upwards, and follow the current. Watch out for the spiked balls and the gaps in the wall. If you are pulled into one, you will be throw back out to the big entrance lagoon type area with the pirates in boats.

Jump up and enter a door on the ledge to be in an area with spiked balls and a jail cell tpye structure with a heart piece in it. Climb up the set of stairs and use Goron Link to smash the barrels, then step on the switch and roll back down before the door shuts to get the heart.

Climb back up the stairs, and smash the barrels on the edge of the ledge. Fire an arrow at the metal plate you see, then jump in the water as Zora Link and swim out before the grate that opened closes. Follow that corridor, watching out for the gaps in the walls again. In the next room, hit the switch to make the metal plate visable, then stand on the little drain thing and fire an arrow at the plate so a column of water will lift you up. Fire an arrow at the plate in the next room to open the locked door.

You will be on the wall back in the entrance lagoon place. Follow the path and you will actually be inside the fort. You need to sneak past all the guards and up the ladder in the middle of this map. When you get to the top, sneak past the guard on the tower and across the bridge. If you can't sneak up the ladder, you can snipe away the guards with an arrow to knock them out temporarily. You will see a small scene with the leader of this band at the top. Shoot the beehive through the bars into the room to make all the guards run away, then jump down and get the Hookshot. Now is a good time to go back to day 1, but you aren't quite done with this area yet.