After the chiefs settle their feud and open Jabu-Jabu's Den, you have to fight the Impostor Jabu-Jabu.
How to Defeat Impostor Jabu-Jabu
First Phase
Jabu-Jabu will first spit out a lot of water, along with things like Tanglers, a small boat, a lilypad, and a grilled fish.
Then Jabu-Jabu will reappear at a random location underwater and swim around, breaking any floating platforms that he hits.
Then he reappears in the middle of the north part of the area, and takes a deep breath, pulling in a lot of water and the objects in the water. If you aren't able to swim away, you'll end up in Jabu-Jabu's mouth and will lose health.
Try to drop a Bombfish into the water as soon as Jabu-Jabu takes a deep breath. The Bombfish will explode and temporarily stun Jabu-Jabu, and some energy will come out. Pick up the energy and switch to swordfighter mode to hit Jabu-Jabu while he is stunned.
Second Phase
After you hit Jabu-Jabu enough times, he starts swimming around while chomping. He will destroy most of the platforms and monsters in the water. Stay out of his way to avoid getting eaten.
Then when Jabu-Jabu takes a deep breath, create a Bombfish for him to swallow. Collect the energy that he drops, then switch to swordfighter form and hit him repeatedly.
After the Battle
Afterward, there will be a cutscene. After the cutscene, go north into the water. Check on the glowing spot in the rift, then check on the opening in the rift to go in. You'll reach the Stilled Jabul Waters.