I had this problem in my wife's 2000. You can fix the problem yourself with a little patience. The drain tube is not findable by looking under the car, it's on top of the exhaust behind a heat shield.I had this problem, after a rain storm. I dried out the footwell and unblocked the drainholes. However I now get water leaking from the grey foam that appears to be an air filter in side the joint running from the fanbox into the heater/ac unit? Is this accumulated condensation from the AC? There is no condensation dripping under the car with the AC running, and there is a steady flow of cold clean water from this joint. Pretty conclusive to me.
However, I can not locate the AC drain tube under the car to try to unblock it?
I found some tree debris in the pollen filter where the rain water had flooded into it because of the original blockage, so is there a danger of debris clogging the heater/ac ducts? If so how to clear it?
1. Remove the passenger seat. (Two bolts at the base of the front seat and three wiring harnesses)
2. Remove trim around carpet and seat belt anchor.
3. Remove glove box.
4. Peal back the carpet and drain the water out of your TCM first (black box-open it) if it still works at this point. You should take it out and dry it in a bag of rice.
The drain tube is between the center console and the glove box way up in the corner where it is almost impossible to get the carpet out of the way. There is one bolt that will allow you to pull it from the hole in the floor/firewall and clear it. Some people have a clog, some folks have had the exhaust melt the end shut. Use a vacuum to suck out the tube.
Leave the carpet up and drain the spongy material. I tied the carpet up to the "oh ****" handles up top and let it air out. Leave it up long enough to drive the car around a few days to make sure this fixed the problem. I have had every single water issue available to this model car. It sucks.
This is my last Audi.