I have a 2002 Honda Civic EX. The trunk is separated into two sections by a horizontal divider. In the bottom section, there's the spare tire, jack, and tire iron and the body of the car. Over that section is a divider made of Masonite (or some similar material), a mat covers the Masonite, and then the top section is where you put your suitcases or whatever.
When it rains, water accumulates in the very bottom section. But the top section never gets wet at all! I went out immediately after a hard rain storm yesterday and felt around in the top section: dry as a bone. I pulled up the Masonite divider and there's a couple cups of water in the bottom.
The weatherstripping does have some worn/torn places around where the trunk closes, but I would think that water leaking in that way would get the top section wet too. The car does have a sunroof and I've read that some sun roofs have a drain that leads to the trunk, but I didn't see any tubes or anything when I was inspecting the bottom half of the trunk.
Any ideas on where this leak is coming from?