2003 A6 water problems

This will be the 2nd time in 6 months that I have run into this problem. I first found it when I went to change a flat tire. There was about 3" of water in my spare tire well. I bailed everything out and dried it out as good as I could. The interesting part was that nothing else in my truck was wet. It looked like the water had just appeared in that area. not even the hard foam around the edges of the well was wet. I figured it was a fluke until yesterday when I was detailing my car. Again the tire well was 3" deep in water.



I'm lost as to what to look for. The two rubber plugs in the tire well seem to be in good shape and I have no idea where the water is coming from.





HELP