Check your cowl area, under the dash where the fan connects to the bottom of the cowl is where you get your fresh air for your fan. If the hoses that let water out of the cowl area are clogged water will collect under your cowl (the part between your windshield and the hood) and it will come through under the dash where the fan connects. I know this because my car had this problem and when I took out the fan to clean it up there was rust in that area.
so to test it out spray water down into the cowl area and if you see the water level rise or that no water comes down the side of your car near the bottom of the fenders it probably means the hoses are clogged with leaves or whatever. Also if this is your problem you will have to remove the dash, atleast to have easier access to the fan area but you might be able to do it without removing it.
Hope this all made sense and helps out.