The water inside the car is coming from a loose drain line on the A/C. This issue is not that uncommon.
The drain tube
is located toward the bottom of the fire wall in the engine
compartment. There are several U shaped cut outs. Two of them are going
to be bolts. The other one is larger of the three and has the drain tube
behind it. There is a rubber flap that covers the tube
You'll need to hold the lid up, and use some kind of pipe cleaner, or
wire to get the gunk out. Might have a splash of water on the ground.
Depends on how much water is backed up in the system. Some people get
between a few inches to a half a gallon.
Here is a diagram (#3 is the drain tube)
Once you have drained the A/C water, you still have to do something with all of the water in your floorboards. If it stays in your carpet, two things will happen:
Dry the carpet as mush as possible, as soon as possible. You may even need to pull the carpet up (carefully, there is a soundproofing material underneath) and let it dry outside of the car. While that carpet is out, look for any rusty spots in the floor. If you find any, treat them with Permatex Rust Treatment. Prepare the surface first according to the instructions (very easy) and spray the Permatex on the bad areas. It will dry into a black coating that can be painted or left as-is. It actually converts the rust chemically into a primer.
I know it sounds like a lot of hassle, but it is worth it to have a dry, clean-smelling car. Spend a couple of hours doing this and it shouldn't be a problem for a long time to come.