As the two Rob's above have said, it will be coming from the pollen filter seal or Plennum Chamber ( the area that the battery & brake servo sit ).
I'm assuming that the car is parked on an upward slope so the water is draining & accumulating in the back.
There are 2 drains, one under the battery & other under the servo. They get blocked & can stop water draining which, if it gets high enough, eventually finds its way into the passenger footwell, or drivers footwell via a cable/ bonnet release grommet hole. Check there is no water in there.
The pollen filter housing needs to be removed completely & all the crud that has accumulated behind & below it removed.
Under the housing is a slot for the seal, which if original, will have disintegrated as it was made of unsuitable foam rubber. VW will sell you a modified seal made of solid rubber that shouldn't disintegrate.
Once you've stopped the ingress of water you will need to tackle the clean-up operation.
It's best if you can remove the carpets for drying but not an easy job.
The convenience ECU lives under the passenger floor carpet & will be sitting in a pool of water. You can just about get to it all by removing the floor trims at the passenger door & left side kick pannel, then mopping up the area carefully.
But I have found after doing several that its best to remove the passenger seat, cut accross the carpet where the ventillation trunking exits so that the whole passenger carpet can be removed.
Under that is very thick foam which will be holding several pints of water.
Carefully check all the wiring to the CCU ECU, open it up & mop up any water that has got inside.
Probably best to disconnect one battery lead first & don't turn on the ignition until the seat is replaced & all airbag system connectors re-connected.
Edited by dieselnut on 11/02/2015 at 11:41
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