Water keeps filling up under passenger seat in rear of car

Correct.
The ac runs in defrost mode to help dry the air blowing on the windshield. The cabin has too much moisture in the air.
You need fresh outside air and it needs to be dried by the ac to work correctly. So if the cabin air filter is dirty you would not get enough fresh air.

The serpentine belt routing diagram on a 1999 VW Passat 1.9 TDI - 110 HP



CS = Crankshaft
F = Fan pulley
Gen = Alternator
T = Tensioner
AC = Air Conditioning
PAS = Power Assisted Steering
WP = Water Pump

Belt routing diagram for 1997 VW Passat 1,9 TDI:


CS = Crankshaft
F = Fan pulley
Gen = Alternator
T = Tensioner
AC = Air Conditioning
PAS = Power Assisted Steering
WP = Water Pump

rhd/under passenger seat.lhd under drivers seat.

all sunroofs have drain pipes, usualy 4, one on each corner, they usualy run down the A pillars at the front and poke out near the kick panals by the footwell. the rears often run down the C pillar to the vicinity of the boot.
open the sunroof up and carefully pour lots of water around the drain gulley of the sunroof, you should see it pissing out onto the floor at the front and rear on each side. make sure water goes down all 4 corners of the sunroof and check. Pipes can come of at the roof. also the drain grommets block up.

common problem on passats also is the pollen filter housing letting in water (under the scuttle panel beneath the bonnet. on left hand drives though, this fills the passenger side only (left). not sure on RHD which side pollen filter housing is on , but when they leak the water fills up inside the car on one side only, which can flow front or rear depending on car being parked up or down hill.
the seal between the pollen filter housing and the bulkhead often leak, if you press down on the plastic housing you may hear the seal squelching water. there was a recall on this, so it may have been done.
If the comparment under the panel (where the battery is) is filling with water, there is a drain grommet under the batter that also blocks up sometimes, causing it to fill up and flow in where it shouldnt.

drill a hole through the floor as a quick fix ,if it gets in let it out ,then check for the leak ,try under the firewall where the AC drain pipe is ,it could be the same pipe for drain water coming in from air intake vents

check under seat, there are 3 sets of wires, they could be coroded, these wires run all the windows door, any thing that is for useing the power, i know just had it fixed 245, 00 later,,

where your battery sits look inside there maybe some twigs and leaves blooking the drainage holes look all along there i had similar problem on vw passat no arm in looking hope this helps?good luck

There may not be any other way to fix it except to replace your instrument panel. That's where your immobilizer is located. Or you could try this:

Try cold-booting the car. Remove both battery cables from the battery. Short the battery cables together (away from the battery) for about 15 seconds. Reconnect the battery. No guarantees - I found this info at tdiclub.com.

if its got a sun roof check the drain pipe from that it may have come off