Trunk leak
#4
also check the air outlet thats where i just fixed a leak on my 2dr. its on the drivers side on the left you have to take off the bumper to see it or take off the trunk lining. but you can only get it out by taking the bumper off.
#6
+1... Also, inspect if you see any type of moisture near the tail lights. My tail light gaskets for the trunk lights are garbage and leak a little water.
#8
Trunk leak
A little late but here is another possibility if you have a sunroof....
https://www.hondacivicforum.com/foru...ighlight=trunk
https://www.hondacivicforum.com/foru...ighlight=trunk
#9
I have a 2000 civic 2dr and it leaks in the same spot as the picture posted. I thought it was the tail lights replaced the gaskets and still leaked. I got in the trunk and had a friend run water down the back window and it came in where the metal is joined. I used so seam sealer and the leak went away. Water leaks suck to trace down.