Have you had the same problem? I cant seem to find out where it's coming from... any suggestions?

 

I had the same problem my self, water was getting in on the right side of the trunk and it was a little hole under the right rear fender, so everytime it rained the tire was splashing water into the hole which ended up in my trunk and into my spare tire. The best way to check for under the car holes is go under the car at night or dusk with a flash light and flash it on your fenders, and at the bottom of your trunk while someone else is looking out for holes where the light penetrates. You can easily fix up holes with silicone. Bad/old/cracked rubber gaskets can cause water to leak in your trunk and also where the pannels meet there can be gaps. A good way to check this is to pour some water and see if it enters through the panels.
If you have rust in your trunk make sure you sand it down and get rid of it, otherwise it will spread even if you fix the leak, moisture from the atmosphere can help spread rust if present, slowly but surely.

 

another way to check ,is to give a flashlight to a friend , then toss them in the trunk & close it , then you turn on the garden hose & spray the back of the car , starting from the bottom & work your way up , when your friend starts yelling he's gettin wet , you found your leak



dont laugh, i've tried this many times , it works

 

Try pulling the rubber gasket off and see if there is a hole.



That's what happend to my trunk, the edges under the rubber seal got rusted that water was getting into my trunk.[&:]

 

Sunroof drain tubes are also a poroblem at times.
And like gsumano sayed about his car. Rust begats rust. If you don't stop it, all of it.... it will come back.
An area to check is where the H2O runs down the back glass, and when you open the trunk, it gathers arouind th trunk opening then rols down each side of the trunk
Check this entire area. Pull the rubber clean/ repair rust, and get some weatherstrip adhesive ad put the rubber back on.
You sunroof tubes ifyou have em.... blow em out with hi pressure air hose.