I had water coming into my trunk via the pressure valves in the bottom of the rear quarter panels, behind the trunk lining. Would find water in the spare tire wheel well. There is a tsb or information from GM about it, which lists all of the possible reasons campb292 mentions, plus the wire grommets and the pressure valves. I believe I found it on this forum, but googling it would likely also locate a copy if you wanted to read it. Was pretty thin of content regarding how to fix—just showed what the problems may be.
Specifically regarding the valves, they may have been installed poorly, leaving a gap for water to leak through. I sealed mine with some silicone but I think the problem may be with the valve flappers themselves. When the car is moving, those valves would be open so air getting into the cab has a way out the trunk. One would think the air exiting would be of enough force to keep water from entering but I still think water may be flying up from the rear tires, right against the flappers. Bad design in my mind. If you pull out the entire liner, you will see the pressure valves. Even if you just remove the pins holding the liner at the rear of the car, you can move the liner enough to see them. Because you have water on the top of the liner itself, I would not suspect the valves in your case, or any wire grommets or other things under the liner, so the other options are more likely.