After finding it odd that there was water under my tool tray the second time, I investigated further pulling up the trunk plastics and the seal around the trunk, and pulling the tail lights for inspection. There ended up being about an inch of water in the bottom of the trunk under the plastic. It is drying now and I will reassess but It looks like only a little bit of surface rust which I will spray with some rust inhibitor. The other alarming area was under the trunk seal. I believe the corners to hold water and allows some to trickle inside the trunk. By the latch, there was also some surface rust as well under the rubber.

I am also going to pull the bumper to inspect the rear vent which is prone to faliure and a source for leakage. I will adjust my latch to close tighter and apply shin etsu grease to all seals.

Anyways guys, check your trunks

 

It's likely the rear air outlet on the rear driver side wall of the trunk. It's common for them to leak.

 

Hopefully, So far that seems the most probable cause for water under the plastic. Just not sure how water got ontop of the plastic under the tray :s

guys check your rubber seals as well!

 

It's a path for water on the outside of the seal. If the outlet is sealed water runs around it on the outside wall onto the ground. If not, it gets inside the trunk.

I had this issue and sealed it from the inside.

 

Thanks, yeah i sealed around the vent but was still getting decent amount of water. Upon further inspection it appears water coming from under the soft top dripping near shock towers. I cleaned out my soft top vents and have yet to check again.

 

I believe there is a sticky in the FAQ about this. There are apparently 3 areas for the water to get in. Lets us know how you make out.