I've checked the forums, and although many have similar problems I am having the main one at the moment I haven't seen anything about.

Ok, so just over a week ago my phone fell into some water, it was submerged for 2 seconds at the most but killed the phone seconds after anyway. I pulled it apart as much as I could to dry it and a few days later got it working again for a while via reflasing until the battery died for good.
I just got a new battery online and since I have gotten it my phone has died within half an hour after a full charge each time. It displays a full battery icon the whole time until after a while it suddenly goes to zero and my phone dies again.
Other than that the phone works perfectly. If anyone can help it would be much appreciated.

That rather sounds like your new battery is crap. Did you check with an original nokia battery? Perhaps somebody you know has a nokia phone with the compatible battery (BL-5J).

My guess is that either your phone is working normally, or it wouldn't work at all. Any power leakage would yield far more serious results than bad battery life (tho I'll happily stand to be corrected).

The battery I got was genuine I made sure of that, but yeah I guess I can never be too sure if it's a dud or not. But considering my original battery simply doesn't work at all no matter what, the fact the new one at least allows me to use my phone fine for an hour or so confuses me a lot.
My friend has an N900 but I can't really consider testing his an option anytime in the near future.

I've heard that a new battery will only reach its full potential after 3 or 4 full cycles of charge/discharge.

Short circuit

Thanks for the replies. Still as confused as ever though :S
It completely died again, but when I use my old battery while charging it the light stays orangey green, while when I use my new one it stays on solid green but either wont allow my phone to turn on.
I think it's safe to say RIP N900. I just wish I knew why it was acting weirdly between batteries.

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!