Hi Wayne,
I checked for Technical Service Bulletins (TSBs) for your vehicle to see if there are any "known" problems with water leaks. The only bulletin I found was about the sunroof (if equipped) leaking into the passenger compartment.
Since there are no known problems for leaks in the rear, you will just have to do some diagnosis. Water leaks can be very evasive. They can originate in one place and accumulate water in another place. Here are some tips:
First, check the seals around your rear door and window. If there are any cuts or damage to the seals, this is most likely your problem.
You may need to remove the inner trim pieces from both the door and from the vehicle sides. Then run a hose over the top of the vehicle and over the rear door to see if you can see any water running on the inside. Be sure and look for water coming down from the roof area. Sometimes the mouldings and sealing material along the roof seams will leak. If this is the case, it will run down the inside wall and end up in the spare tire well. If you cannot find it this way, it may be necessary to remove the seats and ALL the inside trim so the headliner can be removed. I have seen roof leaks that are originating near the front that follow the roof reinforcement channel all the way to the rear. There are holes in the roof reinforcement chanel where you can look inside with a mirror and a flashlight (the headliner must be removed for this).
Another likely place for a leak is along the sides of the roof where the roof racks attach (if your Jeep is equipped with them).
If you find a leak in one of the seams, it is best to repair it with some (water-based) tub and tile caulk or (oil or water-based) plumber's dope. It is not recommended that you use silicone based RTV sealer because this contains acids that can cause the sheet metal to corrode and you will end-up with a worse problem in the long run.
I hope this helps you to get it figured out.
Sounds like either the body has rusted through, or there is a leak up above dripping down onto the carpet.
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