Water leaking into rear well.
My 05 Sienna started leaking water into the rear well on rainy days. At first I thought it was the Large Gasket that goes around the tail gate opening. After carefully examining the gasket and finding no breaks or flaws, I have come to realize that the leaking was around the exterior light just above the rear windshield glass. I sealed it with clear sealant and no more water. I also put some CRYSTAL kitty litter in a pillow case and left it in the rear well to dry out the area. That seems to be working well also. I read that someone else on this forum said he tried everything on his 06 leak in the same area and then tried sealing the exterior light. So thanks for the hint. I also put a bead of sealant around the rear washer nozzle since it is right next to the oblong rear light. Just saying.
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The source appeared to be the larger of the two electrical "raceway" grommets at the top of car, between the liftgate hinges. The seal was just terrible where the grommet met the body of the Sienna.
Took some Gardner-Bender Duct Seal and applied it around that grommet, and the other smaller one also, to be safe.
I just happened to have some Duct Seal around. This is exactly what electricians use all the time to seal things like the service cable entrance on top of electrical meters outside, even though the package says it's for indoor use (in some small print on their product sheet). G-B is probably just protecting themselves from lawsuits, because the stuff just works real well for that. It's soft and pliable, kinda like Play-Doh, but it never dries out.
So far it's working for me. Just happens to be raining now, but when it's dry outside I'll probably apply this stuff to the top grommets (on the liftgate itself) as well.
NOTE: the area should be wiped dry and free of dirt or dust when you apply it. It doesn't stick well when the surfaces are wet. In case you're curious, as I've got it applied, the liftgate doesn't touch it at all when it closes.
BTW have now put a couple thousand miles on my Sienna and I love love love to drive the van. I have had prior experience driving these, so I'm not surprised. When I don't need the cargo space, though, I typically drive my "old" 03-04 2.4L Camrys, coz they get better mileage - no surprise there either. Hope I don't have any further water leaks.
You can get Duct Seal easily at big-box hardware stores or electrical supply stores. And it's really cheap. Comes in 1 lb. bricks for about 3 bucks.
Disclaimer: I don't work for them or have any other financial interest in the product. And as usual, your mileage may vary.