Ark Chests
1. Ark Chest
Enter the pipe and follow the path forward through the sanctum until you reach a dead end. Use the valve on the left to open the door. Proceed through the door and jump down into the hole to find the chest straight ahead in the middle of the room.
Storage Containers
1. Storage Container
Enter the pipe and follow the path forward through the sanctum until you reach a dead end. Use the valve on the left to open the door. Proceed through the door and jump down into the hole. Fight all the enemies and proceed into the tunnel the big dude came from to find the container in the mutant gunk.
2. & 3. Storage Containers
From the previous container, open the valve and proceed through the door and up the pink ladder to find both containers at the top.
4. Storage Container
From the previous containers, enter the doorway and follow the path to the end. Climb up the pink ladder to find the container half submerged in the water near the exit valve.