I suspect that rainwater is collecting in the convertible top storage well and overflowing. Where would I find any drains that might be clogged?

 

Did you find your answer. Just purchased a low mileage B6 A4 Cabriolet and the passenger side rear floor gets very wet when it rain. Also when washing the car. Haven't had much time to investigate further.... Any help would be appreciated. Thanks

 

I got rid of my problem, before having a chance to fix it by wrecking my 06 and replacing it with an '08 B7 with 26K miles!
It turns out that the previous owner had the same issue and had a local repair shop deal with it.
If you cycle the top until the tonneau raises, you will see a drain under the front (both sides) of where the cover seats. You will see a drain hose below it leading to the bottom of the car. If you get under the car (use jack stands and be safe) you should see where they drain, just forward of the rear wheelwells, probably covered up by mud and road dirt. This seems to be s common issue. My foot wells were taking on an inch of water!

 

Thanks for responding, I'll take a look at the drains hoses tomorrow. That would make sense, I haven't had the water problem since the first 2 times, but it has only drizzled, never a hard enough rain to fill a drain channel and back up into the foot wells. I'll post any results and include picks if I can to help any one else. Thanks again.