I have a 98 Accord EX that had water in the trunk and then all over the interior. It was a result of the Sun roof drains leaking into the interior by the drivers side kick plate and the drain tube going into the trunk. First find a diagram of all the 4 sun roof drains and tube routes. The link below only shows 2 of the 4 drains, but there's one at each corner. The main problem was a combination of clogs in the drain tubes and the tube lines being too short and not fitting into the boot carrying the water to the exterior of the vehicle and therefore dumping into the interior.

http://www.myhondapartsstore.com/myh...FcqY4AodGnoA5Q

The first fix was to clear blockage in the tubes, I did this with a weed whacker string. It's long enough to get through all tubes and soft enough not to puncture the tube itself, get a spool so you know it's long enough don't force anything and basically fish the string pushing any debris out where the water goes. My tube on the drivers side front was not long enough and barely fit into the boot carrying the water out. I removed the kick plate held the tube into the boot and placed silicone caulk around the tube and boot in hopes of keeping them together so the water doesn't constantly dump into the interior.

Did the same for the trunk and thus far "fingers crossed" it was solved the problem. Because of the massive amount of water and water in the vehicle prior to pin pointing the problem, the carpet was wet/dry/wet and had quite an odor. I used a Green Machine to clean the interior/remove the water and lifted all mats/carpet and dried the car as best as possible by leaving carpet up and doors open, of course due to the length of time with doors open I disconnected the battery so as not to kill it.

That's my story, what a pain due in part to sloppy work at the factory (tube too short) Safe to say I'll never buy a vehicle with sun roof if I can help it, I've read of similar problems with my 2009 VW Jetta, if you want to see the sun/moon wait till you get out of your vehicle!

 

Yea they can be a pain....but when it is nice outside I like to have it open

What I have found with them is the valve at the end of the hose will clogg. Find where the valve "pokes" out of the body and then insert the weedeater line from that end.....be carefull, once the clogg is gone water will come out so don't have your head right under there.....guess how I know that

To get to the front ones you have to pull the inner fender back......

Now that you have them clean you can pour some water in the moonroof channels and see where the water is coming out of the "body".