Many folks have posted stories about Prius II roof body weld leaks in Prius Chat Rooms like PriusChat.com. I was finding the same problem in my 2009 Prius. For us the many contributors on PriusChat honed in on just the source of the leak and helped us a lot.
We had been getting water in the spare tire area and then this winter Toyota told us the battery froze up as it was surrounded by a frozen block of ice. They said “keep an eye on it.” Not helpful.
It got worse and finally after 3 days of rain and a soaked car we had to dig in and find it. This was on April of 2020.
After quite a lot of looking we decided we needed to take out all the rear trim. Not simple:
We Checked all the usual places and nothing seemed to show. Then following leads from PriusChat we tried using a pitcher of water running water down the roof drain gutter. If we ran the water from hinge of the hatch or lower, no leaking occurred. If we ran it from higher up the rain gutter, like over the rear door entry, as shown here, it leaked!
Upon deeper investigation, we think we found the spot, the same type of seam crack under the mastic on the rain gutter down near the hatch.
It may be there and elsewhere so we applied silicone to the seams of both left and right rain gutters from rear door back to below the clip for plastic.
It is now 5 months later with no water accumulation. I agree with the disappointment about Toyota. We expect to run these cars over 200,000 miles and over 10 years. That’s why Toyota commands top dollars. At least the dealers need to be aware of this.
THanks very much for the time and effort other PriusChat contributors took to share this with us.
PS. I tried Toyota’s TIS Site and a two day rental of repair manual to learn how to remove the trim. (see reference picture below.)
Very glad I did that.
Here's What I Found 