Please check your luggage compartment. Mine had standing water for years (so it appears). The amp and woofer bases are completely rusted. I came about it while trying to troubleshoot my speaker problem. I believe the leak comes from the upper driver side hatch access for wiring (liftgate, third light etc...). The water appears to enter around the rubber seal and flow behind the lining making it's way down to the well. Based on the discoloration of the lining it must have had several inches of water at some point. I have yet to test the amp and woofer but being partially submerged I am worried they have been damaged...Hence the speaker problem from another thread of mine.
Anyway, if you're on warranty, please take a look so you can have your parts replaced before it's too late....