After the Zora chiefs argue at Crossflows Plaza, they chase after Jabu-Jabu.

Follow Jabu-Jabu

From the entrance of River Zora Village, go east and up the slope, then go east to find a house that was destroyed. Go north from there, into the archway in the cliff wall. Then go east through a hidden passage. You will find Kushara and a River Zora in front of the rift, which now has a glowing spot on it. Approach them and there will be a cutscene.

Check on the glowing spot in the rift, and there will be a cutscene. Then check on the new opening to go in. You'll reach the Stilled Upper Zora River.