2010 Prius - water leak into spare tire well

If you lift up the hat seal a little bit they're up around the shocks and up around across the top you may see some cracking in the putty or whatever the stuff is that Toyota uses to fill around where all these welds are done . You see some of it in the floorboards underneath the carpet etc etc In the trunk you'll see it If you hit it with a hammer it breaks up cracks because it's all dry and brittle You have something similar running around the hatch where the lip for the seal is welded on or pin welded in place whatever sometimes that stuff will get to cracking You can literally see it It looks like cracked paint but that's not what it is water can in grass through those little cracks drip into the trunk area generally right on top of the battery usually or right at the trailing edge of the top of the battery which is towards the back of the trunk water will hit that run down pool in the well sometimes it gets over on the battery side too the 12 volt fills that well up freezes and kills your 12 volt happens all the time I drilled extra holes small ones near where my 12 volt sits because their place where it can pool I also removed a rubber plug on the 12 volt side now I never see any water In that area anymore The first year I had the car like a month after I bought it I lifted up the cover for the 12 volt and saw it sitting almost in a brick of ice well that was no good.

 

Have you pulled off the black rubber strips running the length of the roof? IIRC there were reports of leaks there.

Also leaves can get in behind brake lights, possibly divert water in.

 

Did you check for a deeper water puddle in the corner near the lead-acid battery? Rainwater off the roof and hatch will run into that corner of the interior when the drain passage between taillight and body sheet metal clogs. I had to remove the taillight to unclog mine.