'88 big water problem

I'm curious ... Has anyone had to fix a Cherokee water problem? I recently replaced the weatherstripping because I've had problems with water soaking thru the carpet. This weekend while replacing the seats and interior trim I lifted up the carpet to find that there was a bunch of water sitting on the floarboard. Both sides, front and back, and the matting was soaked. I used a shop vac on the matting to suck up as much water as I could and this morning, still had water in the carpet. I couldn't see where the water was coming from and it looks like there's no place for it to drain. It also looks like it gets trapped under the heavy rubber carpet backing and can't evaporate. Is this common enough that someone might know the best places to look for the leak(s)?