The fresh air vent and the heater assembly both have a area where the air is brought in from the cowl area, both have a built in drain. Now both sides did what paccool said and filed the foot area with water and did rust/thin the floor in my truck out. If you open your doors and look through the jam toward both these vent area there is a small crack in the bottoms to let the water run out, if plugged then it floods everything. There is an approx 1. 5" area between bottom of outside vent area and the vent itself. Mine were super plugged with leaves, a bird nest, a glove, and those helicopter seed things. I just stuck a screwdriver in there and opened it up a bit, and flused it out. If you leave them plugged it would hold the water and rust it out, as well as flow into the area where the floor meets the kickpanel area and rust it out also. BTW I know as I just fixed the floor! And the insulation was rusted into the floor. No insulation going back in only rubber.
Someone also said the cowl cracks can also leak onto the floor, I havent checked mine yet.
Jlast