I would suggest resealing the vapor barrier in the door first. I had a leak I thought was coming from my door seals, but it was from the vapor barrier. Resealed it and it was water tight once again!

 

Smileybug,

Thank you for the reply and I will certainly check that.

I presume from your reply that seals for the doors and rear hatch are not easily available or not available at all?

 

Its not something I've really looked into. I started looking for mine for my GTI and found some but I didn't look for them all. But doing the vapor barrier is pretty much free. No reason to buy new seals if they aren't the problem. They certainly could be, but I would start with the easiest first.

 

The majority of leaking in our '98 and '01 beetles is from the ledges on left and right corners of the engine compartment under the windshield wiper valance. Drain holes there get clogged up by leaves, and water comes through firewall and under carpet and can make both the front and rear footwells quite wet. It's hard to access under there but I use vacuum cleaner attachments, chop sticks, etc. Have fantasized about making custom screen overlay to keep leaves out but have never attempted. Also I try to park with the front of the car angled down if I have the option. Other trouble spots are 3rd mount stop light and hatch emblem. Finally, sunroof drains must be snaked regularly with weed eater line.