Plenty of stuff falling out of trees + rain = water on the floor boards. You have plugged drains somewhere.

I had to do this today. Remove engine compartment rubber gasket, remove plastic cover up near the wind screen, and pour about one gallon of water down into the space where the batter sits. Did it drain quickly, or not at all? If not, remove the battery and feel around for the drain hole under the battery stand. push the junk through the hole. Now, feel under the brake master cylinder. Do the same thing as there is a drain under there. Problem solved. For sun roof, read elsewhere.

2004 A4 1.8T auto
160,000 miles

2000 A4 1.8T 5sp
216,000 miles