Okay.... Eran from CC might be able to explain in more detail how my Honda Tech and he found out where my water leak in my Civic coupe is originating from at least. So maybe this will help you.
I've seen a tiny bit of water in my car before. Nothing really major though. I used fabric cleaner on the spot on the trunk "floor" and it's been fine since. No smell, nothing.
Well, just since moving to WA it's began leaking again. Just since we got it back after it was stolen. So it's only been leaking around a month maybe. And a lot. I opened my trunk to see about half an inch of water pooled on top of the fiberglass (whatever the "carpet" stuff is made out of on top of the cardboard-like covering in the trunk of the EX). I dried the trunk as best as I could, but the water kept collecting over the next few days. We stripped the entire trunk so that nothing woudl get damaged as badly (use a clip remover, found at Autozone or similar stores - it looks like a door handle puller, only longer). Just looking in the trunk and where the water was falling and soaking into the cardboard, it looked like it was dripping from the top middle of the trunk seal. Come to find out... that's probably just where it would condense, and then drip from.
We ran a hose over the car and THOUGHT the leak was coming from two tiny pinch welds right on the outside of the trunk seal. I'll try to remember to go out and take photos to better explain this later, since you have the Civic sister car, and well, some things will at least be similarly built. The water would drip from inside, on the "top" of the trunk right about in the middle along the trunk seal. Checked the seal too, it was fine (inspect yours carefully for cracks and splits though).
Later, my Honda Tech decided to try once more to make sure that's where the leak was coming from. We didn't want to use the epoxy and end up still having a leak (it's kind of like silicone when wet, but dries as an epoxy and would have filled the inside chamber in between the body panels with the leaking seam). So he put my car in his garage at his house, took a small space heater, plugged it in and shut it in the trunk of my car. We went inside and waited for EVERYTHING to dry off.
When the entire car was dry, they took a cup of water and poured some near the top of the trunk, where we thought the leak was. It didn't leak. So they dried it off and poured the water at the top of the window. It leaked. Then they dried everything again and moved between those two spots, from the bottom up.
Found out my leak is actually the rear wind shield seal, right along the driver's side. Not AT ALL where we had thought originally.
So my tech is getting me info on the body shop they use for such problems. I'm lucky, my water leak will probably cost me no more than $200. Some water leaks cost up to $5000 though. I also learnt that 2005 Ridgelines are having water leak problems (in the wheel well I think.. they close it entirely up so that it's quiet in the trunk, but water collects in there... guess it's not as closed as they think... so they have to drill a hole in the bottom to drain it).
Anyway, I hope this might help you some and sorry it's so long winded. I wanted to explain everything we had done though. My tech also said my leak was probably started by an accident in the car's past, and these things pretty much just take time to mature into a noticeable leak.