I had a problem just like this very recently. After buying my car it rained, and when it cleared up I went to install my sub in the trunk, only to find a pool of water in the spare tire compartment. At first I thought it was a sunroof drainage tube, because one was disconnected. The other day, after more rain, I noticed the pool back again in the trunk.
After taking the interior panels off, folding down the seat, and liberally spraying a hose on the outside of the trunk, then peering in to try to see leaks, I found my culprit. It was near my driver tail light. I thought it was the seal, but under closer inspection, I found a crack in the body. It looked like it had been repaired before, so I threw some sealant in, let it dry and put the tail light back on. Hasnt rained recently for me to find out if its thats it though.
So, it could be your sunroof drainage tube, bad seals for your tailights, or (less likely) a crack in the body
If you have the time, you may want to take the panels inside off, and have a friend spray the back of the car while you look inside to see any leaks. Good Luck!