Others may have had this problem. I found a couple of gallons of water around the spare tire, down in that well.
Where is it getting in, and how do I stop it?

 

Which model?

 

If its anything remotely older its usually rear light seals. Of course I'm going to assume you've gone to the effort of identifying whether the boot seal itself is in good shape or not given it will have been right in front of you.
If its leaking so badly that you have a small swimming pool in the boot, the entry point/area should be fairly obvious and easily traceable - just run some water over the back for 30seconds, open the boot and you'll likely spot where its coming in.

 

On ours it was the seal sealant up near the boot hinges.

 

I’ve fixed a couple of these, the usual culprit is the mastic type sealant that’s in the boot shut at the end of the roof rail the 1/4 panel joins the roof, around the hinge and under plastic strip on the roof and they are absolutely notorious for leaking, just pull up the roof rail, clean out as much of the bad sealant as you can and then tiger seal it up and tiger seal the roof rail back down, job done. Obviously check around the rear lights, as well but I pretty much guarantee it’s the sealant being cracked beside the roof rail.