I have an Audi A6 2006 quattro. Start noticing driverside front and back foot well soaked in water after rain. Most likely from the roof drain clog.

A few weeks after and one more rainstorm, I noticed the crank weak and struggle before going through and starting the car.
Then next day my car wont crank.Everything turns on, so battery is good.

I lifted up the carpet and saw the control module, which seemed dry
Anyone have any idea what could have received water damage under the carpet preventing the car to crank?

 

I have the 2002 audi a6 4.2 and had the exact same problem. My water got in through drain holes on the bottom of the battery tray being filled up and just running straight through the firewall into the foot well.

I had to replace the Comfort control module and the Transmission control module, also had to check to make sure no water go into my ECU which is right next to the battery.

I personally had little problems here and there until I finally just pulled up all the carpet and re-did the interior wire harness. That only took a weekend to get done. Just remove both seats and the trim. Carpet comes up easy and goes back down easy.