'01 4Runner, water sloshing in liftgate

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KLF

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Friend visiting for the week, she has an '01 4Runner. When I started to open the liftgate to get her bags, she warned me to stand back. Sure enough, a bunch of water poured out as I opened it. She said its been like that for a few months. She said the rear window is no longer usable, it goes down crooked. When I slammed the gate back down, you can hear water sloshing inside.

I have no experience with these models, is this a common problem? What am I in for? I told her I'd try to fix it.
 
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I recently had the same problem in my front passenger door. Removed the plug to drain it but couldn't figure out how it got filled up with water. My gaskets around the window are good and the window was closed when it rained. It has happened twice but has been through heavy rains an hasn't happened since. Still not sure how it got filled up. I would check the gasket around the window as a starting point.
 
There are 3 drains in the bottom of the hatch - clean them out using a ziptie end. If the hatch is full of rust chips and leaves, remove the inner cover and vacuum the junk out, after it dries.
 
Epilog: tore it all apart. As much as I disliked liftgates before, now I hate them even more. PITA.

Apparently she drives a lot of dirt roads, she lives in Fredericton, NB. Truck has ~250K miles on it, and it gets oiled every year. So no rust on the body anywhere. The weatherstrip part that sits at the bottom of the window was caked with years of dried fine silt, it could no longer keep water out. But there was a bunch of silty mud down inside the liftgate as well.

There are actually 4 drains in the bottom. One pair at the seam at the very outer corners, and a pair of plastic plugs snapped into ~1/2" holes. The plugs have little bits of foam in them, and I believe they are supposed to allow water out but not in. Well, the silty mud had clogged everything. So I cleared the outer holes and removed the plastic plugs entirely.

The loose window was caused by one of the arms in the regulator, the little ball-and-socket joint at the end of the arm was all rusty and it separated. I was able to get it back together, but it won't last. Her hubby owns a repair shop up there so she can get parts at cost, so I unplugged the motor and gave her a printout of the diagram from the EPC with the part circled that she needed to replace.
 
Good work. Toyota always designs body drain holes like the only thing that would ever pass through them is filtered, distilled water. If you live in grimy country, you need to make changes (as you did), to the body drains.
 

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