My 06 mustang keeps getting water under the carpet on the passenger side ?

The cowl drain is clogged. This happens over time. I had the same issue and checked, yes the cowl drain system was clogged. You can do it without removing the cowl covers. I found this out when I got to the drivers side and didn't want to remove the wiper assembly to clean it. There is a rubber flap in the center of both sides. When you find it you can clean it out. You can easily remove the passenger side cover and clean that out first. What happens is that when the passenger side gets clogged the water raises above the cabin filer and then gets into the car.