Water only in the back floor

Check where you 12v battery is located, rain also accumulates in that spot too... Because it's hard to see down in there maybe use a stick and see if it comes up wet... As for where the leak is coming from, the most common place is where the black gutter strips on the roof of the car pop off and you can clean underneath... The seams where the metal panels join together in that area going down the back channel of the hatch are where it most often comes from. Possibly debris build up keeps the seems wet and it deteriorates quicker / starts to leak.

 

Time for the "dollar bill test"!

Working around the outer perimeter of the door, close the door with a dollar bill (you can obviously use any US bill, but the neighbors and SO's might raise an eyebrow at a c-note ) between the door and body overlapping a little each time. If you can pull the bill out w/o much (any) resistance, that is where the problem is likely to be.

Aside from the door frame seals, there is really no way for water to get onto the rear seat floor, except an open window.

 

READ this thread: Water leak...into spare tire area etc | PriusChat

You might have this problem. People have posted good pictures tracing the water entry and their repair.​

Nearly all of the water intrusion I have read has been for these two reasons:
1) small cracks in the body joint sealant (or whatever it is called) at the roof line near the rear hatch hinges (L & R).
2) recent body work

Door seals would be first for me. But that is possible. It should be easy enough to rule out w/ visual inspection and a hose forcing water along the perimeter. All the times I've washed the car and put high pressure along the perimeter, occasionally A FEW drops might enter.

 

Curious what your outcome was? I have the same issue happening. Thanks!