2010 Prius. Was having water pool in auxiliary battery well, and also on the much less deeper area on the opposite back corner of the car. If the water gets too deep on the driver side back corner, it will flow into the tire well. The source of the leaks was the same on both sides. It was the seal to the lower rear lights. Must have gotten old with age. There are two nuts on each back light that you can tighten up to try and seal it better. I used some silicone caulk to seal those areas as well. If the light housing needs to be replaced due to damage, I can just cut the silicone off. Below is a picture before the sealing that shows where the leak was on the auxiliary battery side. Make sure to put screens over those back vents. Mice intrusion can do a hell of a lot of damage to your car: Mouse proofing with caulk and screen.
I had the same problem, caused, or at least aggravated, by dead leaves and other tree-associated trash getting stuck between the body and taillight housing. Water coming off the roof effectively drains through that space, a truly dumb design feature, in my opinion.