I've still been dealing with the leaking trunk on my 2002 LS430. I think it has something to do with repairs that were done wrong/poorly in 2009, when it was in an accident involving the rear passenger side of the car. The rear glass was replaced, among other things. This has been driving me crazy since I got the car in November, and I really want to finally fix it. Luckily, the water hasn't damaged anything, including the radio tuner and amplifier, even though I'm pretty sure it's been leaking for years. There was an inch or two of dirty water in the spare tire well when I found it... yikes.

I replaced the tail light gasket because it was folded over a little and couldn't make a good seal. It still leaks, but at least I know it's not that now.

Yesterday, I pulled out the rear seat cushions, and there was some moisture starting near the passenger side seat belt. The recycled foam padding behind the seat (not in the actual seat back) was damp. It looks like it's been leaking for a while, as the metal frame on both cushions has rusted pretty badly on that side only. I never actually noticed any moisture in the car, but it's definitely getting in.

I suspect that the rear window has a leak in the seal, and that's letting water get into the area under the deck lid (I think that's what it's called). Does anyone know if this is a possibility? I put everything back together already, but I can get back in there and take pictures if it would help.

 

Update: turns out it was leaking from the top passenger side corner of the rear window. I think some dope did a crappy job replacing it.