There are six keys: one in the central tower in the passage underneath the floating platform, the one in the medium level of where you met Ruto (east bottom) and need to bomb a wall, the one in the passage with the gate and eye switch, the one at the end of the river after longshot that also has a gate and eye switch, the one in the room with swirling water that you drop into from the end of the river after the longshot (you can get this one much earlier from the bottom west), and the one in the room past where you met Ruto (bottom east) that you open by lighting torches on the bottom floor after lowering the water.
It's not impossible for glitches to happen, but I would check the key behind the bombable wall and the two keys that are near the end of the river after the longshot (behind gate and eye switch and the one in the room with swirling water and the dragon looking statue that has a switch to hit with the hookshot/longshot underwater).