There are several places where the Civic/CRX EF chassis tend to leak. After 20 years the seam sealer is starting to dry-rot and develop hairline cracks for water to leak in through.
Finding a leak can be very hard to do...
The best way to identify where a leak is coming from is to disassemble the interior panels of the area in question. Then get inside the car and have a friend wet the car with a hose on specific areas. Try to wet each area one at a time so that you can narrow down where the water is leaking in. Because of folds in the sheet metal etc. it may be impossible to see the actual leak. You have to understand that water will trickle down behind panels and become visible in a completely different area of the car. Once you have identified where it is leaking you can use the appropriate method of re-sealing it.
The correct way to repair these types of leaks is by using a wire brush and drill, and grind off all the old seam sealer in the area. Then apply new seam sealer and then paint if needed. Or if you are a broke student like me, you can just silicone over the cracks (I like the high-temp RVT black silicone). It is important to really clean the area and let it dry to get the best seal possible adhesion.
The infamous hatch shock area where water collects
1. Sunroof and drain tubes
- The drain tubes can be clogged with debris like sediment and leaves which will prevent the drain pan from draining. The pan fills up and spills over on you as you drive to work in the morning. The tubes can also become disconnected behind the paneling and fill your trunk with water. You should remove the interior panels and disconnect the drain tube from the drain pan. Use compressed air to clean out the lines.
Here is a nice write-up: https://wwwx.cs.unc.edu/~hays/crx/crxsunroof.pdf
Here is a write up on how to remove headliner: http://crxcommunity.com/viewtopic.php?t=1340
Civic hatch sunroof drain tubes
2. Rear washer nozzle gasket (on the roof)
The symptoms are leaking into the hatch shocks area and down the panels into the trunk. You can create your own seal or use silicone to seal the nozzle down. To remove, use two old “credit cards” and slide them from front and rear to depress the retaining clips.
3. Roof drain channels (under the black trim, each side of the roof)
This usually appears as water collecting in the hatch strut area, and the seam sealer wears out. The entire section of seal can be a problem but the rear corners are especially notorious for leaks. Use silicone to seal the hairline cracks in the seam sealer.
Here is an excellent write up on that: http://www.crxcommunity.com/viewtopic.php?f=10&t=10036&start=125
4. Rear Tail light gaskets
Over time the tail light gaskets dry out and crack allowing the leaks. You can make your own gaskets out of foam from a hobby store or apply silicone sealant around the edges your old one. then reinstall while silicone is still tacky.
Here is what it looks like when the gaskets leak and the water leaves marks on the chassis
Clean the old gasket. Apply silicone to the sealing edges and reinstall tail lights.
5. Rear hatch mounting hinges
Usually the seam sealer is dry and cracked and all it takes is a small hairline crack to allow a leak. You can remove the hatch and strip all the old seam sealer and redo it all or silicone the edges of the hatch hinges.
Here is a write up: http://htarchive.org/showthread.php?t=2222273
(You can do a cleaner job than this guy)
6. Windshield seal
When the windshield seal goes bad it will usually leak in the front foot well area on the side that has the leak.
7. Front Cowl Area and Hood Hinges
Seam sealer here can go bad here as well. Water can also leak in through the “fresh air vent” located under the cowl on the driver’s side. You can remove the fresh air vent and clean it and silicone it down.
Driver's Fresh air vent
Passenger Fresh Air Vent Inlet - I just discovered this one in a strong downpour the other day. It started leaking from behind the glove box and dripping on the carper just in front of my ECU. After I removed the cowl I could see the wet areas and how the water got in. The problem was the plastic clips that are the "screw anchor" for the hood cowl (yellow arrows). They were old and dry rotted and cracked. It is hard to tell from this pic but they are directly above the opening in the chassis that pulls in fresh air. I also sealed the plastic cover panel (green line).
8. Antenna Seal
The water usually trickles down the inside of the pillar and results in a leak on the drivers foot well.
9. Water leaking in through Front Speaker
Usually the plastic water barrier has been torn and allows water in through the speaker grilles. To fix it, remove the old plastic sheet and trace it onto some new plastic liner material and cut it out and attach. I used plastic “drop cloth” material from home depot but almost anything will work.
10. Door Hinges Area - (Not a common problem..........yet)
I actually saw these pictures and thought it is only a matter of time for all of us.
My hood hinges