1999 Honda Civic EX. 2 Door. Sunroof.
If your civic trunk is leaking it may be the bumper cover support bracket.
Remove the trunk carpet kit to access the bracket connection inside the trunk. If it is leaking you will see a trail of dirt down the trunk wall below the bracket.
If it is the next step is:
Step 1: Remove the Bumper Cover
There is a plastic part that holds up the bumper cover that started leaking when the civic was 17 yrs old. I call it the "bumper cover bracket".
The bumper cover is that semi-flexible plastic cover over the actual hard rear bumper parts. It can be removed by removing a couple screws in the rear fender well and some clips in the trunk.
In photo 1 the white part is the bumper cover bracket. It holds up the bumper cover. The bumper cover hangs on it. This photo is directly behind the wheel well on the side of the car.
The black thing on the right is a vent for when you shut the door the pressure escapes out this vent.
The black tube on the left is the sunroof drain outlet.
The green wall is the outside wall of the trunk. It is single wall. The green toward the lower part of the photo is the bumper cover. In this case, I only partially removed the bumper cover and wedged a 2x4 between the car and the bumper cover so I could access the parts. After doing this I would recommend just removing the bumper cover and do both sides (it would be much easier).
Step 2: Why Did It Leak?
Photo 2 is the bumper cover bracket removed. You are looking at the back side. To remove it you must get behind the carpet kit in the trunk and give the fitting a little squeeze with pliers or needle nose. There is a thin rubber washer between the trunk wall and the back of the bracket. I figure this washer has deteriorated from its original condition and this was not the best engineering. Also, the weight of the bumper cover pulls the bracket out away from the outside trunk wall.
Whatever! This is where it was leaking. I used a liberal amount of 50 year black silicone caulk and reinstalled the bumper bracket.
I also removed the sunroof outlet and siliconed it back in too. It
was not leaking, and is a better design, but I figured it might start leaking. Inside the trunk and behind the carpet you will see the clear tubing that runs down through the roof posts from the sunroof to the sunroof outlet. Mine was pretty dirty because I have a lot of tree trash here. I pulled the tubing out of the outlet and cleaned it out.
Step 4: Inside the Trunk
Photo 4 is the inside of the trunk behind the carpet kit. The sunroof outlet has already been removed. The white square is the bumper cover bracket. The black thing on the left is the vent.
Photo 5 is the clear plastic tubing from the sunroof drain. It plugs into the sunroof outlet. The reddish thing is a bucket I had catching water while cleaning it.