Why water in a VW jetta wagon?

Check around window seals common problem on those.

If you have an electric sunroof, you may have plugged roof drains which cause rainwater to back up and run down your headliner, down the roof pillar and into the passenger seat floorpan. (Speaking from experience). VW had a recall for this very problem so, take the car to the dealer and have the roof drains cleaned out and updated to alleviate this from happening again. The repair is free.

This problem occurs in VW's I've owned ranging from 1999-2006 Jettas, Golfs, GTIs and Passats and the different has never offered to fix for free. I was only ever successful in clearing the drain (accessible on my 2001 Jetta when sunroof is open) and shooting air (from a gas station) down the hole that i guess leads under the car.

You almost never will know this is a problem under after rainfall and if your car is parked outdoors during the rain and you come back to your car and notice a gigantic puddle on ( for some reason on mine, always the passenger side ) floor.