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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.
There are drains for the sunroof that are located in the coners of the roof, these plug up and the water drains into car, you will need to remove the cover were the seatbelt is and see if the hose that connects to the drain fell off or if drain is plugged, open the roof all the way back and using a bottle filled with water , pour over the drains one at a time and see if it drains if not you will need to use a coat hanger and unplug them but i would still check for the hose off on the side that leaks water. good day.
There is a great possibilty that there is a leak on the Left Side of the Windshield. It is most likely in the area of the upper left side.
The reason for this conclusion is:
The rain water is coming in the Left Upper Side; and either coming down the "A" Pillar, or traveling underneath the trim on the inside roof and coming down the "B" Pillar.
The only other explanantion is a torn, worn, cracked or dislocated Weather Seal on one or both of the doors, allowing rain water to come in. Inspect very carefully these Weather Seals, especially on the top front portion of the rear door.
To help you locate these after a hard rain:
Take the trim panels off the "A: and "B" Pillars and the Roof Line above both Doors. Check for wetness underneath the trim. Or take these trim panels off, and place folded paper towels under the trim panels; reattach the trim panels and wait until it rains. Afterwhich, take these trim panel off and check the paper towels for wetness.
The Windshield Seal is easily inspected for cracks and tears.
Let me know if this helped, or if you have additional information or questions. Feel free to contact me at FixYa.com!
That's usually easier to do if you remove one side rail. There are usually six access holes in the rail that the screws go into. (pretty sure the screws are torx type) Once the rail is off, you can easily attach the cross bars and re-attach the rail to the roof. Ends of cross bars are held on with a screw that goes in from the bottom side. When replacing roof screws it is good to put a dab of silicone sealer on each screw hole to prevent rust or leaks.
You likely have a water leak around the 3rd brake light mounted on the top rear of the cab. I had this same issue on my 96 Ranger Supercab and found that the foam seal had gone bad and was allowing water to leak into the back of the headliner around the light fixture. It ended up soaking the headliner from one side to the other as the headliner acts as a 'wick'. You can repair this issue by either replacing the sealant around the 3rd brake light or replacing the brake light. There are two screws which secure the 3rd brake light assembly to the back of the cab. Remove these and it will pop right out. I upgraded mine to an LED light when I replaced it. That solved two issues at once as I'll never need to change a bulb there again. If you want to be cheaper you can not replace the light and just seal it with rubber silicone sealer.
I turned on the fan inside and closed everything up, went outside and poured soapy water around everywhere. I found bubbles at the mirrors and and the top of the windshield. Also a "Tech" told me that under the door rubber at the driver and passenger sides there is a piece of tape that is supposed to cover two assembly holes on either side but doesn't, so I caulked it and solved the leak that comes out the map lights. I also found that there was a crack in the sealer along the firewall to passenger inside fender allowing water to collect int the wiring channel causing the dreaded "lock" problem, which I had fixed by the dealer but they didn't fix the leak. The dealers and "Jet-set Execs"are the reason GM is hurting as their vans are OK. The fix was spraying RV Roof\Gutter sealant from the front after removing the wiper cover and spraying waaay in. Now I need to fix the one on the front that comes in above the passengers left foot and makes a spiders haven behind the centre cowl. Jim
your footwells will fill with water - even under your seats right to the back seats footwells
See two 10mm holes in front sides when sunroof is open.
a) push a flexible cable down from the top - it comes out just behind the front wheels. (use electric three core cable - or TV aerial cable - a hanger is too short) - you need about a metre and a half)
b) remove the inner mudgaurd behind the front wheels (2 screws) you will see the end of the plastic drainage pipes - remove the blocked black rubber cup at the end of these - why they are there is anybody's guess)