Rep Power: 0

I have a 2001 Civic Ex and I've had the trunk leaking for some time whenever it would rain heavily. I never found the reason why until I looked in my trunk today and found a wet spot and this rust. I'm certain this is what has caused the leak. I don't think it's bad but I don't want this to get worse. So are there any suggestions on what I should do?

 
Rep Power: 211

You jump in the trunk with a flashlight, close it and have a helper spray the rear window and trunk down with a hose. This will help isolate a leak(s).

That spot in the image is pretty rusted so you need to pull the trunk seal and find out if it's rusted through or can be repaired without cutting out metal and replacing.. I would assume the rust may be worse under the trunk seal as it can capture moisture when the area around it starts rusting.

If it isn't completely rusted through you can wire brush it, wet sand it, and treat it with Ospho rust treatment (rust to black). Once the Ospho cures fully (a week or so) you can paint over it with a primer and top coat.

You may need a new trunk seal and 3M Weatherstrip Adhesive (black)
Sometimes the back window seal under the trim can be the issue as well.

 
Rep Power: 134

A couple more ideas are that it may be leaking around that passenger side (I think by the photo) tail ight in the chassis (not the trunk lid) - may need some silicone to seal a leak.
The other thought is there rubber stoppers in the trunk lid that you can adjust to seal the trunk when closed. Perhaps they counter-clockwise too much and a gap exists such that rain infiltrates your trunk? Again I would concentrate on the passenger side according to your photo.

 
Rep Power: 0

I finally got a chance to look at it after all the wet weather in NYC and it's not looking good. I tried taking off the rubber seal and it's rusted through.

 
Rep Power: 0

It's going to be raining for the next few days so I've tried to cover the rust as much as possible to prevent more water from coming in, but I'm not sure where to go from here. Metalwork isn't really my thing lol

 
Rep Power: 224

Oof, that looks bad. I've never seen one of these Civics rust there. The only way to fix it would be to cut out the bad section and weld in a replacement. You would need a body repair shop.

 
Rep Power: 211

You could call around to local junk yards and see if the have your generation of civic. If they do ask them if they cut out sections of their cars for replacement purposes.
Other option is to bring a battery power grinder (and back-up batteries) and cut out a section that will match your trunk's area of concern.
Cut a section out of the junker that is a few inches bigger all the way around than the area on your car. You can always cut down the replacement piece but you can't add to it so... oversize accordingly when you cut it off the junker.

Bring it to a welder that will tac-weld it in and then you bondo, sand it as needed. It looks like the rust area doesn't extend to the body, and if that's the case it shouldn't effect the way you car looks other than inside the trunk. After bondo then sand, prime, paint to help keep rust from returning.

Please post more pics: top views, side view, underneath the shows the whole effected area.

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Rep Power: 0

I'll see what junk cars I can find around since they're fairly common and get someone to cut out a piece. I haven't had the time until now to really work on this but I'll take more pics tomorrow and keep y'all updated

 
Rep Power: 211

You may want to bring by a local body shop first to see if their opinion aligns with mine. You don't want to make a mistake you can't recover from.