I have recently have an ongoing problem with water under the mat in the trunk after driving in rain, It's both sides too. Any suggestions ?

 

Are you saying the top of the carpet isn't wet, the water is coming in from underneath? If it's leaking from above, check the holes for the bolts on your spoiler to see if it's leaking in around them. The only other places I can think of are the holes for the tail lights and third break light.

 

I'd check in the trunk area for leaks around the body seams. I had some in mine:

 

Is it happening on just one side or both sides? I remember reading on another forum that one guy had a leak from a bad seal where the fuel filler neck went through the quarter panel.

 

I waiting for the rain to stop here in the Pacific NW to check it out !
I've pulled the rubber plugs from the rear wheel wells to drain the water

 

finally got a dry day and I took my trunk apart
and it appears the water leak was around the third taillight
the seal there was nonexistent

more later !