This is a pain-in-the-ass!
What happened to me is that every single time I returned to the car after it had been out in the rain and lifted up the boot door to put my stuff in, three or four (or more!) pints of water came pouring out the bottom of the boot door.
The angle it was parked at seemed to be a factor.
I've been looking for another car for a while and at least one of those I looked at had the same issue.
Some helpful previous owner of my car had taken out the two trim screws holding the boot door liner in place at each bottom corner. This allowed the water out, but I'll bet there are loads of cars suffering from the same issue and it's just sloshing quietly around in there? -or not?
My own car had recently had the boot door lock changed-no doubt due to the water ingress (not cheap!) and the 2001 A8 I looked at whose boot door was full of water, needed a new boot lock as it's had failed too.. Prolly worth checking if yours is watertight esp. if you keep it outside.
Anyway, I tried everything to fix it, mainly concentrating on the area where the rear number plate holder fixes in. The rear light clusters got a lot of attention too. I suspected the replacing of the boot lock might have not been done properly so I spent ages checking this out. Some of the threads in the five bosses that the screws go into on the number plate panel were stripped. So I built these up and retapped them and carefully sealed up any likely holes
Also the frozen water had seperated the boot door skin, along the top seam where it meets the bonded in ally piece that forms the rebated area where the rear number plate goes, so I had to fix that and seal it, and double-double check it as it seemed most likely to be the root of the problem. But still it leaked.
This went on for months- the actual boot was dry but the water always poured out when I opened the boot door, wetting the boot carpet.
I'll spare you all the investigative details, but it turned out to be the cable grommet located at the o/s front corner of the boot door. This had perished (although strangely the one on the n/s was ok.)
I got it with some RTV and the boot's been dry ever since.
