If there's a short circuit in the phone drawing power, and you left the battery in after the phone shutdown due to low battery, you're likely to destroy the battery. If the circuit board inside the battery has been damated by water it'd explain the different behaviour.

The charger chip itself can only produce one colour on the led, which would indicate that in one of the above situations the software is alive and in the other it's maybe not alive. Or, the OS is unable to communicate with the charger chip.

Any case, orangey green suggests damage around the 3 circuits controlling the notification LED, or possibly around the charger chip itself.

That was the nerdy n900-autopsy reply, here's the normal reply:

Dude you submerged your N900, hope you're insured!