The flooded vault is a room containing a large metal door identical to the Alpha 2 basement door. It is different from the other flooded room in that it is completely underwater, and cannot be accessed in its flooded state. There is another room behind it which was empty until Beta 3, where it contains a bear rug and a guitar.
Alpha 4, Beta 1 and Beta 2
It could be drained via a valve on a ledge at the side of the house. In the Betas, it was the location of the Fear Factory level which would unlock the superthrow ability.
The flooded vault appears, but instead of containing the Fear Factory level, it allows access to the guitar used in unlocking the cage with the generator. It can be drained in the same way.