Instructions
Go to Great Bay Coast and equip the Zora Mask. Swim to the northern edge of this area and sink to the bottom. Locate the four boards on the wall, and then press "A" to ram the second board from the left. This uncovers a secret entrance. Proceed inside.
Enter the water in the next area. Swim to the left, avoiding detection by the patrolling guards. Locate the platform here and exit the water to find a Goron Switch. Equip the Goron Mask and activate the switch to open a gate below the surface. Equip the Zora Mask again and swim through the newly opened tunnel.
Head forward and around the corner. Smash the board in front of you, and then push or pull the block. Go left and make your way around, breaking the pair of boards. Push the next block when you reach it, and then go right and up to the top-left corner. Swim above the sewage pump and it will carry you to the next area.
Stay low and avoid the water mines here. Climb out when you reach the other side and head through the door. There are more water mines in the next room. Navigate around them to reach the chest, and then turn and head up the ramp.
Go up the stairs and move to the left. Destroy the barrels with rolls or Fire Punches, and then locate the switch on the far left. Activate it, and then roll through the door to obtain a Heart Piece. Step on the switch here to get through the door. Head up the stairway again, and then hit the crystal switch with Arrows or Zora Fins to open the gate below. Go back down and swim through the gate.
Swim through this next area, and then climb the ladder. Step on the switch to expose the crystal, and then run to the inactive water pump. Shoot the switch to engage the water flow. Jump off before you reach the top; there are mines on the ceiling.
Head up the ladder and turn to face the mines. Shoot the one in front of you to obtain a clear shot at the crystal. Hit the crystal to open the door below you. Head through the door and you will be back at Gerudo Lagoon. Move around the corner and up the ramp. Enter the door to gain access to the Pirates' Fortress.