Leak in rear cargo area. (1 Viewer)

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I noticed a smell the other day in my wife’s 100. Searched around and discovered wet carpet under the storage deck I built in the back. It was wet all along the tailgate and damp out maybe a foot into the carpet.
I found a decent amount of leaves around the weatherstripping at the top near the hinges. Thoroughly cleaned it all. Cleaned and vacuumed the carpet and ran a fan to dry it.

Tonight we had a big rain storm blow through. I went and climbed inside the back during the rain and noticed a tiny amount of water showing up in the area shown in the picture. (Bottom of hatch, where it meets tailgate) I could imagine after lots of rain, like we’ve had over the last few weeks, it could eventually get to the carpet.

Anyone else had the same issue? Weatherstripping all looks intact. Could it be the window seal? How do I diagnose?

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take a look at the upper hatch brake light. normally seal degrades and leaks come from there. I had to reseal mine and all is good.
 
As already mentioned above, most likely the 3rd brake light seal. The seal cracks over time and allows water to "trace" down the inside of the rear top hatch trim. That makes its way into the rear carpets after it wicks downward into the lower hatch trim.

Many threads on this, so a search will yield a ton of how to's and more info. I replaced 3rd brake light since Toyota won't sell you just the seal (it comes with the 3rd brake lamp assembly), but there are ways to reseal using silicon if your careful.
 
Thanks for the help! I'll check out the brake light.
 
Does anyone have the part numbers for the tailgate upper and lower weatherstripping? I’ve sealed up my third brake light thinking that was the source, but it wasn’t. I get leaks from the top left side where the wire bundle rubber cover is, but only when going through a no-touch car wash that has jet sprayers. I am thinking I should replace the weatherstripping.
 
Does anyone have the part numbers for the tailgate upper and lower weatherstripping? I’ve sealed up my third brake light thinking that was the source, but it wasn’t. I get leaks from the top left side where the wire bundle rubber cover is, but only when going through a no-touch car wash that has jet sprayers. I am thinking I should replace the weatherstripping.
Partsouq will have the part numbers. It's worth entering your VIN, so that the site will automatically pull up the parts drawings for your specific rig. Those weatherstrips are in the body/exterior section under the back door panel and glass subsection. 6828160020 and 6788160110 for my '99 (manufactured 10/98) for the upper lift gate weatherstrip and back door weatherstrip.
 
Does anyone have the part numbers for the tailgate upper and lower weatherstripping? I’ve sealed up my third brake light thinking that was the source, but it wasn’t. I get leaks from the top left side where the wire bundle rubber cover is, but only when going through a no-touch car wash that has jet sprayers. I am thinking I should replace the weatherstripping.
Have you removed the wire bundle cover before? If it's been removed before it needs to click back on when it's put back or it'll leak.
 

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