Okay, I've done a search and apparently on the A6 Quattro this is a common problem. Well I did a little troubleshooting and it turns out that my drains are not clogged up.
I had a windshield installed about a year ago and not sure if this has anything to do with it or not but I noticed that the black plastic shield that connects at the bottom of the windshield doesn't block water from going underneath it. As a result, water flows under the plastic piece and right into my cabin filter housing.
Does anyone know if this piece is replaceable and if so is there an online source for it?
Thanks

That dosen't sound right... Is the plastic piece broken?

If it is out of the sight I would consider using a bit od silicon sealer to keep the water out of the filter housing.. But I would look elsewhere fora leak.

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1997 A6 Avant
1998 Jetta
2007 Dodge Grand Caravan SXT
one High Performance Roller Skate

The most common cause I believe is the sunroof drains that get clogged up

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2004 A6 Stg 2+ and 99 TJ...mod