I had this problem when I first got my 93 GXE. Take a look at where the contact strip on the trunk lid from the weather stripping is. If there is a solid line all around your trunk lid the that seal is fine. Then take a look at how the seal sits on the trunk itself. Take a hose and run a slow stream around the outside of the seam to see where it leaks. If there is nothing there, take a look at you tail lights, run the slow stream of water around them to see if that's the culprit. The seals had degraded on mine and thats where the leak was happening on one side. The other had a body panel that had not been sealed properly (after repair I believe) a little RTV should fix the problem. Look for the stuff that is water proof but flexible.
My trunk also gets wet! And it gets all mildew smellin' and stank in there!
The florida downpours have been also filling my passenger side taillight full of water!!!! It got full of mildew in it too. I had to take it off, drain it out and fill it full of bleach and water to kill off the nast crap! It was a mess! Since then the inside of my trunk hasn't been getting wet. SO I suspect my light housing was the cause. This could be your problem too I'd imagine.