I have had this same problem with my daughter's car
My daughter has a 2001 Jetta that had this same problem with the passenger side front floor getting wet. I did several things to try to eliminate this problem and I am guessing that it was probably the cabin filter that caused it. Every year, I change the cabin filters on the cars. You need to be very gentle and careful when removing the plastic cover to get at the filter as it has to be cocked just a little bit and angled just right to remove it without breaking it. The filter needs to be removed with the plastic tray that it sits in if you expect to get it in right and it only fits correctly 1 way. I even removed the housing for the cabin filter to be sure that it was sealed propperly (I don't think this was a problem, and removing it required removing the plastic trim piece just below the windshield which meant the windshield wiper arms had to be removed, kind of a PITA). A small piece of the plastic cover that you remove to access the cabin filter was broken off, I cut a piece of thin aluminum (Home Depot sells thin strips of aluminum in various widths) and used some black paint and black RTV compound to patch the piece that had broken off.
I also checked the AC drain. You do need to access this from underneath the car. There is a flapper perferation in the foil insulation on the firewall under which there is a rubber fitting where the AC coil drains. I used a can of compressed air for cleaning off computers (I had the red plastic tube attached and fit a small piece of very small ID tygon hose just big enough to squeeze over the red plastic tube), the drain opening is up higher than you can probably reach with your arm so I attached the tube to a paint stick and snaked it up inside the AC drain fitting. I don't think the AC drain was plugged, I just wanted to be sure that I ruled it out as a possibility. The can of air did do a nice job of blowing that line back.
If you have a sunroof, I would also verify that all 4 drains from it are clear. There is one in the front and rear of the sunroof on each side. The front drains go to a small black rubber nipple on the front door posts. I use a flower pot watering pitcher to pour some water into these drains and verify that it runs out freely at the nipple. If it does not, kneed the nipple between your fingers as it has a very tiny hole and gets plugged easily (I used a pair of nips to cut a corner off of the end of mine to enlarge the hole).
I have also seen posts in here about people that have had this problem after the door was opened for maintenance. There is a plastic membrane that must be put back propperly or the side doors can leak water in. To get the water dried out I removed the floor mat and put down towells with heavy bags on them to absorb the water. The floor carpet has a pretty heavy rubber backing so it can take a while to suck the water up through it.