I have a 98 wrangler. Every once in a while the passenger side floor gets flooded with water. I have heard from some people that it is that the ac hoses get clogged, but I have only noticed it when it rains a lot. I have some rubber mats, and they stay dry, but the floor under them is soaked with water, so I know its not coming from the top.

I have a '97.  It was the antenna mount on mine.

Does it happen only when you drive in heavy rain, or if it's just sitting in the driveway?

Pete  

I own a 98 and mine was caused by the a/c evaporator line coming out of the firewall. When driving the air caused the a/c drain to blow back into the floor. A simple fix, and one that will eliminate this as a cause, is to go to the parts store and buy a 2ft section of heater hose, attach the heater hose to the a/c drain located on the firewall. Attach it to the drain with a hose clamp and run it down towards the frame. I tucked mine in between the frame and the inner fender plastic gaurd. That way the water drains under the Jeep, and dosen't blow back into the interior.

If this doesn't fix your problem then you can look and more labor entensive fixes like finding a seal leak.

I had this happen on my 6 month old '03.  I had recently gone muddin' and a large amount of mud and sand got thrown up on my hood while backing out of a deep hole.  The debris settled in the vent catch basin at the base of the windsheild, blocking the drain in the bottom of the housing.  When the basin fills with water it drains into the body tub and soaks the passenger side floor.

Remove the sill between the hood and the base of the windsheild and clean out the basin and drain line.  Be careful with the drain, it is thin rubber and will tear easily.

George