Interesting responses. Thanks guys!

I'm going to go take a look at the "nuts" holding the spoiler on and check for rust marks. I'm also going to look for that "little" hole underneath the tool kit, to see if water is getting in there.

Thanks for the suggestion! I'll keep you guys posted...

PS: I am the second owner, but I've had the car almost two years and never noticed a problem before...

 

I have a 2003, bought it new, no spoiler of any kind.
I had the water in the tool area just once, not sure if it was after driving in a downpour or washing the car, dried the well and has not happened again, even though I have washed the car and driven in the rain many times since.
Dry it out and observe when it collects again.
I would agree with the others in that I doubt that it is coming from above. At least in my case the trunk "carpeting" -more like carton- was all dry.
Good luck and keep us posted.