Ark Chests
1. Ark Chest
Enter the tunnel and follow it until you reached the barred section. Take the doorway on the right (south). Work your way through the flooded room and exit the doorway at the end. Turn left and crouch through a shipping container around some mutant growth. When you emerge, head through the northwestern door in the adjacent tunnel to find the chest along the northeastern wall.
2. Ark Chest
From the previous chest, pass through a small locker room, emerging into another section of the tunnel. Follow the path southeast, arriving at another doorway with a green light above it. Head through the doorway to find the chest on the east side of a storage room near some metal crates.
Storage Containers
1. & 2. Storage Containers
After you defeat Smeggo The Vile, head into the tunnel to find both containers near a valve.