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I got this 2004 Civic from my cousins a year ago, and in the last 3 months I was doing work on it and I realized I had a ton of water in my trunk. Where the spare tire sits, that little indention has about an inch of just standing water. It fills up every time it rains, and somehow some of the water goes to my drivers side back seat.

Pictures:
1) https://i.imgur.com/k0ZRJNK.jpg - This is the whole trunk, the spare tire indention has an inch of water that is a bit difficult to see in this, but know it's there. (if you zoom in you can faintly see the outline)
2) https://i.imgur.com/FY51CK0.jpg - This is the very back of the trunk, where more water was just sitting.
3) https://i.imgur.com/naws7C6.jpg - This is my drivers side back seat, and again it's hard to see but it is wet.

So after I realized all of this was happening, I decided to put a GoPro in my trunk and record what was happening, and here is the result (link: https://imgur.com/tUJGq11). You just see all this water rush to the middle of my trunk as I was leaving my neighborhood. Me and my dad went to a car wash, sprayed our hose all over the car, and ran more tests, but couldn't get any water to leak. It literally only happens when it is raining, and we are absolutely clueless as to what the problem is. Does anyone have any idea because I sure don't.

 
Rep Power: 224

Common causes of water in the trunk:

-Sun roof drain tubes clogged (granted you have one). Pull back the lining on both sides of the trunk, there's a clear tube running down to a rubber grommet. If that rubber grommet clogs with debris water will leak out into the trunk.
-Behind the lining on the driver's side there's also an air vent. The left rear tire and pick up water from the road and spray it into this vent.
-Misaligned trunk or bad trunk seal.

 
Rep Power: 134

Tailight lenses leaking?

 
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I too am getting water in my trunk, especially in the well on the left side of the trunk. It's an EM2 from 2003 I thought I fixed the problem by re-seating and clamping the two ends of my skylight drain tubes. But here we are, I'm a little suspicious that the angle that the car is parked at might have something to do with it.