For those with sun roofs, I realize the water can be coming from many sources other than blocked or disconnected sun roof drain tubes, but it just takes a couple of minutes to raise the sunroof to access the rear drains, and move it rearward to access the front drains, and pour water into the drains in each corner. If the water you pour in drains out the front of the rear wheel housing (rear drain holes) or the rear of the front wheel housing (front drain holes) then you know the problem is not with the sunroof drain tubes.
This check is quick, requires no tools, and will help you determine if the water is coming from the sunroof drains or not.
If the problem is with the sunroof drain tubes, the easiest fix is to replace the tubes. If you reach that point and don't know what to do, send me a PM and I will describe it to you.
If the water is not coming from the sunroof, in my experience the next likely culprit is the door water shields. To access the water shields, you have to remove the door trim panels. The water shields are large sheets of plastic that are sealed to the door inner sheet metal with butyl tape (black, sticky stuff). This plastic directs water in the door down to drain holes at the bottom of the door, and keeps it out of the passenger compartment. It is common for the butyl to dry out and separate, leaving a path for water into the car. Examine the seal created by the butyl all around the water shield. If it has separated, you can buy rolls of butyl at any body supply store. Ask for the stuff used to install windshields in older cars. If you install new butyl, make sure you don't cover the three drain holes at the bottom of the door, on the inner face. The butyl goes below the holes, not above, so the holes are contained in the area of the water shield that is sealed off from the passenger compartment.
I don't have experience with fixing trunk leaks, so if the sunroof and doors are not the source of your leak, let me know what you find and how you fix it.
2001 Bonneville SSEi (retired at 365,000 Kms.)
2014 Jeep Grand Cherokee Overland (yes, I know its not a GM)