Hey all, I finally found the source of my massive water leak! Ever since I’ve owned this car (bought it for $875 from a copart auction, see my thread) the car kept fogging badly and getting a bad musty smell. I would ozone it only for the smell to return. Finally last week I removed all the trunk trim. My battery was submerged entirely in water and water had spilled into the spare tire! I drained it all out with a shop vac. Two weeks later? Battery was half submerged again from rain! I popped the roof trim/seal up and sure enough tons of body cracks. For $5.19 at truevalue I bought some cheap caulk and slapped it all over the cracks with my finger. We’ll see if that holds! NOTE: cracks were present on both sides of the car! Here’s pics: iPhone ?
Thanks for this post and the pictures. My car's hinge area was okay, but for other readers, also check the rear brake light assemblies. I think mine were allowing water under/into them. Also there are little horizontal weld/crease/metal joints on the inside of the car, bumper area facing forwards on both well sides (mine was wettest into the battery area). I used similar caulk to caulk where I could clearly see water dripping in. That plus caulking where the light assembly plastic presses up against the hatchback drain area has kept the battery and first aid well sides of the car dry. If you still get water, check the wheel well to battery well wall and make sure that's tight.
Edit: several years later, I had to go back into the back of the car and the battery - and found that the busbars had corroded, so I cleaned them off (big job, as you have to remove the battery and carefully do a lot of the same steps I did when I repaired the battery modules. Anyway, I noticed I was getting water like the OP. Today, I pulled off the roof gutter covers (the long black stripes that go from windshield to hatchback. I have nearly identical cracks to the OP's. I used some semi-dried up similar GE caulk. We'll see if my work was enough in rain soon. If not, I'll hit it with better caulk, but this issue is very likely on most Gen 2 Priuses, so do pull the gutter covers if you don't see cracks under the hatch!