I had the same issue on my rear drivers side floor. It was because the drains for caught water were clogged, so water overflows.
Here's a pic:
Water comes in by the rear window and falls into there where it drains out via drain holes in the frame in front of the rear wheels. I would get some water under the back seat too because of this. What I did was pull the rear interior, seats, speaker, and also the front seats and such so I could pull up the carpet enough to clean under there and silicone any holes water was coming in through. lower the convertible, have the rear windows up, and I mixed all the chemicals I could find and sprayed it in there and let it sit. Then the drain holes I gave the coat hanger treatment but I suggest pipe cleaners. Stick a hose in that area to rinse everything out and repeat. I even attached a rag to a broomstick to wipe in there. It looks cleaner down there and after 10 rains my drivers side floor doesn't get wet anymore, but I'm going back and 100% finishing it by sticking the pressure cleaner rod in there.
When you have everything pulled out stay in the car while someone gets at the outside with a hose so you can identify where water comes in and floods.
The picture of that mustang I attached shows were water comes in and is supposed to go.
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