The only way you'll find it is by sitting in the boot while someone sprays a hosepipe over the car so you can track it in.
Mine does exactly the same, I think it's the rear light seals, and it has led to the first bit of actual rust on the car (I'm probably going to cut it out and weld it over the summer). It's less of a problem in my car though as I have stripped out the boot (and shortly most of the interior again) and have drilled a hole in each of the rubber bungs in the boot floor - that way if water does get in, it'll just drain back out again