Go back to Almera's house and board the raft to the west.
Use your rope on the rock to the south.
Use your rope on the dead tree next to you.
Enter the door.
Head down the eastern passage and search the darker crates for a key.
Head down the western passage and go north.
Use the key on the door.
Use the key on the next door, as well.
Use an air rune, a water rune, and an earth rune on each of the six pillars (make sure you've one of each rune on each pillar, as the room will flood if you do not perform this step fully before doing the next step).
Access to Waterfall dungeon for training, WARNING! You must have Glarial's amulet in your inventory for re-entry to the dungeon. If it is destroyed or lost, follow the steps in quest to get another amulet. (Attempting to enter without the amulet will result in the tunnel flooding with water, you getting washed into the river, ending up on the bank and taking some damage.)